diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 636d9c75dcb3907911b74a291911a2020bb0f322..085078bf8ca9a2d98667e28292967d5823de4621 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,32 +40,32 @@ create_graph:
paths:
- workflow.svg
-deep_run_workflow:
- stage: test
- image:
- name: kaczmarj/apptainer:latest
- entrypoint: [""]
- tags:
- - custom
- script:
- ## Downloading apps
- - mkdir appimgs
- - apptainer build appimgs/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest
- - apptainer build appimgs/pan1c-env.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cenv:latest
- - apptainer build appimgs/pggb.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/pggb:latest
- - apptainer build appimgs/pan1c-box.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cbox:latest
+# deep_run_workflow:
+# stage: test
+# image:
+# name: kaczmarj/apptainer:latest
+# entrypoint: [""]
+# tags:
+# - custom
+# script:
+# ## Downloading apps
+# - mkdir appimgs
+# - apptainer build appimgs/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest
+# - apptainer build appimgs/pan1c-env.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cenv:latest
+# - apptainer build appimgs/pggb.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/pggb:latest
+# - apptainer build appimgs/pan1c-box.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cbox:latest
- ## Running workflow
- - mkdir -p data/haplotypes
- - cp example/*.fa.gz data/haplotypes
- - HOME=$(pwd)
- - rm config.yaml && mv example/config_CICD.yaml config.yaml
- - apptainer run --bind $HOME:/root appimgs/pan1c-box.sif snakemake -c 4
- artifacts:
- paths:
- - output/pan1c.pggb.03SC_CICD.gfa
- - output/pan1c.pggb.03SC_CICD.workflow.stats.tsv
- allow_failure: true
+# ## Running workflow
+# - mkdir -p data/haplotypes
+# - cp example/*.fa.gz data/haplotypes
+# - HOME=$(pwd)
+# - rm config.yaml && mv example/config_CICD.yaml config.yaml
+# - apptainer run --bind $HOME:/root appimgs/pan1c-box.sif snakemake -c 4
+# artifacts:
+# paths:
+# - output/pan1c.pggb.03SC_CICD.gfa
+# - output/pan1c.pggb.03SC_CICD.workflow.stats.tsv
+# allow_failure: true
diff --git a/Snakefile b/Snakefile
index b1304234749e36e263050cca1bfe24b102887292..81cf6432214f176c39698a892b00b7f9b8a2a1b2 100644
--- a/Snakefile
+++ b/Snakefile
@@ -99,6 +99,7 @@ rule ragtag_scaffolding:
output:
"data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
threads: 8
+ retries: 1
params:
apppath=config["app.path"]
shell:
@@ -110,6 +111,11 @@ rule ragtag_scaffolding:
-r {input.ref} \
-q {input.fa} \
-o {output}
+
+ if [ ! -s {output} ]; then
+ echo "Empty fasta"
+ exit 1
+ fi
"""
rule clustering:
@@ -164,6 +170,8 @@ rule create_sglAsm_syri_fig:
fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
wrkdir=directory('data/asm.syri/{haplotype}')
threads: 4
+ resources:
+ mem_gb=48
params:
apppath=config["app.path"]
shell:
@@ -222,29 +230,169 @@ rule create_pggb_input_syri_fig:
rm {output.wrkdir}/*.fa
"""
-rule pggb_on_chr:
- # Run pggb on a specific chromosome
+# rule pggb_on_chr:
+# # Run pggb on a specific chromosome
+# input:
+# fa="data/chrInputs/{chromosome}.fa.gz",
+# gzi="data/chrInputs/{chromosome}.fa.gz.gzi"
+# output:
+# gfa="data/chrGraphs/{chromosome}.gfa"
+# threads: 16
+# params:
+# pggb=config['pggb.params'],
+# apppath=config['app.path']
+# log:
+# cmd="logs/pggb/{chromosome}.pggb.cmd.log",
+# time="logs/pggb/{chromosome}.pggb.time.log"
+# shell:
+# """
+# /usr/bin/time -v -o {log.time} \
+# apptainer run {params.apppath}/pggb.sif \
+# -i {input.fa} {params.pggb} -n {nHAP} -t {threads} -T {threads} -o data/chrGraphs/{wildcards.chromosome} 2>&1 | \
+# tee {log.cmd}
+# mv data/chrGraphs/{wildcards.chromosome}/*.gfa {output.gfa}
+# """
+
+## WIP - Adding rules to split pggb workflow into dedicated steps
+
+rule wfmash_on_chr:
+ # Run wfmash on a specific chromosome input
input:
fa="data/chrInputs/{chromosome}.fa.gz",
- gzi="data/chrInputs/{chromosome}.fa.gz.gzi"
+ fai="data/chrInputs/{chromosome}.fa.gz.fai"
output:
- gfa="data/chrGraphs/{chromosome}.gfa"
+ mapping="data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf",
+ aln="data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf"
threads: 16
- params:
- pggb=config['pggb.params'],
- apppath=config['app.path']
+ params:
+ apppath=config['app.path'],
+ segment_length=config['wfmash.segment_length'],
+ mapping_id=config['wfmash.mapping_id'],
+ wfmash_sec=config['wfmash.secondary']
+ log:
+ cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
+ time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
+ cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
+ time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
+ shell:
+ """
+ ## Mapping
+ /usr/bin/time -v -o {log.time_map} \
+ apptainer exec {params.apppath}/pggb.sif wfmash \
+ -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+ -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+ --tmp-base $(dirname {output.aln}) \
+ {input.fa} --approx-map \
+ 1> {output.mapping} \
+ 2> >(tee {log.cmd_map} >&2)
+
+ ## Aligning
+ /usr/bin/time -v -o {log.time_aln} \
+ apptainer exec {params.apppath}/pggb.sif wfmash \
+ -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+ -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+ --tmp-base $(dirname {output.aln}) \
+ {input.fa} -i {output.mapping} \
+ --invert-filtering \
+ 1> {output.aln} \
+ 2> >(tee {log.cmd_aln} >&2)
+ """
+
+rule seqwish:
+ # Run seqwish on alignement produced by wfmash
+ input:
+ fa="data/chrInputs/{chromosome}.fa.gz",
+ aln=rules.wfmash_on_chr.output.aln
+ output:
+ "data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa"
+ threads: 8
+ params:
+ apppath=config['app.path'],
+ seqwish=config['seqwish.params']
log:
- cmd="logs/pggb/{chromosome}.pggb.cmd.log",
- time="logs/pggb/{chromosome}.pggb.time.log"
+ cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
+ time="logs/pggb/{chromosome}.seqwish.time.log"
shell:
"""
/usr/bin/time -v -o {log.time} \
- apptainer run {params.apppath}/pggb.sif \
- -i {input.fa} {params.pggb} -n {nHAP} -t {threads} -T {threads} -o data/chrGraphs/{wildcards.chromosome} 2>&1 | \
+ apptainer exec {params.apppath}/pggb.sif seqwish \
+ -s {input.fa} -p {input.aln} -g {output} \
+ {params.seqwish} -t {threads} \
+ --temp-dir $(dirname {output}) -P 2>&1 | \
tee {log.cmd}
- mv data/chrGraphs/{wildcards.chromosome}/*.gfa {output.gfa}
"""
+rule gfaffix_on_chr:
+ # Run gfaffix on seqwish graph
+ input:
+ rules.seqwish.output
+ output:
+ gfa="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa",
+ transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
+ threads: 1
+ params:
+ apppath=config['app.path']
+ log:
+ time="logs/pggb/{chromosome}.gfaffix.time.log"
+ shell:
+ """
+ /usr/bin/time -v -o {log.time} \
+ apptainer exec {params.apppath}/pggb.sif gfaffix \
+ {input} -o {output.gfa} -t {output.transform} \
+ > /dev/null
+ """
+
+rule odgi_postprocessing:
+ # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
+ input:
+ rules.gfaffix_on_chr.output.gfa
+ output:
+ gfa="data/chrGraphs/{chromosome}.gfa"
+ threads: 8
+ params:
+ apppath=config['app.path']
+ log:
+ cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
+ time_build="logs/pggb/{chromosome}.odgi_build.time.log",
+ cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
+ time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
+ cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
+ time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
+ cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
+ time_view="logs/pggb/{chromosome}.odgi_view.time.log"
+ shell:
+ """
+ OGfile="$(dirname {input})/$(basename {input} .gfa)"
+
+ ## Converting to odgi format and optimizing namespace
+ /usr/bin/time -v -o {log.time_build} \
+ apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
+ tee {log.cmd_build}
+
+ ## Unchoping the nodes (merges unitigs into single nodes)
+ /usr/bin/time -v -o {log.time_unchop} \
+ apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
+ tee {log.cmd_unchop}
+
+ ## Sorting the nodes
+ /usr/bin/time -v -o {log.time_sort} \
+ apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
+ -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
+ tee {log.cmd_sort}
+
+ ## Exporting to gfa
+ /usr/bin/time -v -o {log.time_view} \
+ apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ view -i $OGfile.unchoped.sorted.og -g \
+ 1> {output.gfa} \
+ 2> >(tee {log.cmd_view} >&2)
+ """
+
+## ----------------------------------------
+
rule generate_graph_list:
# Generate a text file containing all created graphs
input:
@@ -288,7 +436,7 @@ rule graph_stats:
shell:
"""
apptainer run --app gfastats {params.apppath}/PanGeTools.sif \
- -g {input.graph} -P -o $(dirname {output.genstats})/{wildcards.chromosome}
+ -g {input.graph} -P -o $(dirname {output.genstats})/{wildcards.chromosome} -t {threads}
"""
rule graph_figs:
@@ -331,12 +479,13 @@ rule aggregate_graphs_stats:
--outputPaths {output.pathstats} --panname {params.panname}
"""
-rule gfaTagR:
+rule final_graph_tagging:
# Add metadata to the final GFA
input:
graph="output/pan1c.pggb."+config['name']+".gfa",
output:
"output/pan1c.pggb."+config['name']+".gfa.metadata"
+ threads: 1
params:
apppath=config['app.path'],
panname=config['name']
@@ -365,7 +514,6 @@ rule pggb_input_stats:
rule core_statistics:
# Aggregate chrInput, chrGraph and pggb statistics into a single tsv
input:
- pggbStats=expand("logs/pggb/{chromosome}.pggb.time.log", chromosome=CHRLIST),
chrInputStats="output/stats/pan1c.pggb."+config['name']+".chrInput.stats.tsv",
chrGraphStats="output/stats/pan1c.pggb."+config['name']+".chrGraph.general.stats.tsv"
output:
@@ -378,7 +526,7 @@ rule core_statistics:
"""
mkdir -p {output.dir}
apptainer run {params.apppath}/pan1c-env.sif python scripts/coreStats.py \
- --pggbStats {input.pggbStats} --chrInputStats {input.chrInputStats} \
+ --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
--chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.panname}
"""
diff --git a/config.yaml b/config.yaml
index d3677ba3a71233ce885f79f80e85faf70bbb2637..7780f37515a3d69019c4a9e172c9f37f41f4c34a 100644
--- a/config.yaml
+++ b/config.yaml
@@ -5,6 +5,16 @@ name: '<pangenome name>'
reference: 'CHM13.hap1.fa.gz'
# Directory of apptainer images (downloaded with getApps.sh)
app.path: '<path>'
+
+# Core parameters (WIP)
+# Wfmash alignement parameters : leave to None if unknown
+wfmash.segment_length: 5000
+wfmash.mapping_id: 90
+wfmash.secondary: '-k 19 -H 0.001 -X'
+
+# Seqwish parameters
+seqwish.params: '-B 10000000 -k 19 -f 0'
+
# Optional parameters for PGGB
pggb.params: '-X --skip-viz'
# Odgi 1D and path coverage viz parameters
@@ -18,3 +28,6 @@ get_PAV: 'False'
get_allASM_SyRI: 'False' # All vs all
get_ASMs_SyRI: 'False' # Haplotype vs Reference
+# Debug options
+debug: 'False'
+
diff --git a/example/config_CICD.yaml b/example/config_CICD.yaml
index ccec4c32daa3f4f60d5064351c528f10d7d4fb8b..111a904ade2c07331426caae26a0aa1984d134d6 100644
--- a/example/config_CICD.yaml
+++ b/example/config_CICD.yaml
@@ -1,12 +1,29 @@
+## Main parameters
+# Pangenome name
name: '03SC_CICD'
+# Reference fasta (BGziped)
reference: 'R64.hap1.fa.gz'
+# Directory of apptainer images (downloaded with getApps.sh)
app.path: 'appimgs/'
+
+# Core parameters (WIP)
+# Wfmash alignement parameters : leave to None if unknown
+wfmash.segment_length: 5000
+wfmash.mapping_id: 90
+wfmash.secondary: '-k 19 -H 0.001 -X'
+
+# Seqwish parameters
+seqwish.params: '-B 10000000 -k 19 -f 0'
+
+# Optional parameters for PGGB
pggb.params: '-X --skip-viz'
+# Odgi 1D and path coverage viz parameters
odgi.1Dviz.params: '-x 500 -b'
odgi.pcov.params: '-x 500 -O'
-## Control over optional parts of the workflow
-# get_PAV is very long the more haplotypes there are (all vs all comparison)
+
+## Optional parts of the workflow
+# Computes Presence Absence Variant matrices for Panache (not recommended; very long)
get_PAV: 'False'
-# get_allASM_SyRI controls if the SyRI figure with all haplotypes diplayed should be created (longer with #haplotypes)
-get_allASM_SyRI: 'False'
-get_ASMs_SyRI: 'False'
+# Computes SyRI figures for haplotypes
+get_allASM_SyRI: 'False' # All vs all
+get_ASMs_SyRI: 'False' # Haplotype vs Reference
diff --git a/runSnakemake.sh b/runSnakemake.sh
index 5f63d8d1715590abab5f8cfebd110a5844f67bad..4206dc0ac47eb9ab6ed7e1b4818f8b14e9039a9d 100755
--- a/runSnakemake.sh
+++ b/runSnakemake.sh
@@ -12,5 +12,5 @@ module load containers/Apptainer/1.2.5
# Creating DAG
apptainer run <path_to_pan1c-box>/pan1c-box.sif snakemake -c $(nproc) --dag | dot -Tsvg > workflow.svg
# Running the workflow
-apptainer run <path_to_pan1c-box>/pan1c-box.sif snakemake -c $(nproc)
+/usr/bin/time -v -o whole.run.time.log apptainer run <path_to_pan1c-box>/pan1c-box.sif snakemake -c $(nproc)
diff --git a/scripts/coreStats.py b/scripts/coreStats.py
index c81a347837235f3057e5a8e6194d263b57b87403..91e693fc7aa1bc9bcb03f7c889ead49a48958363 100644
--- a/scripts/coreStats.py
+++ b/scripts/coreStats.py
@@ -24,10 +24,9 @@ import seaborn as sns
arg_parser = argparse.ArgumentParser(description='Pan1c usage stats script')
arg_parser.add_argument(
"--pggbStats",
- nargs="+",
- dest = "pggbStatsFiles",
+ dest = "pggbStats",
required = True,
- help = "Time logs for pggb"
+ help = "Time logs for all pggb steps"
)
arg_parser.add_argument(
"--chrInputStats",
@@ -83,12 +82,15 @@ def getRegEquation(x, y):
## Main script
aggregatedData = {} # Temporary data holder. Will be transformed into dataframe after having parsed every inputs
+PGGBsteps = [] # Storing PGGB steps name
#%% Parsing section
## Parsing ressources usage for pggb
# Iterating through all pggb time stats
-for pggbStats in args.pggbStatsFiles:
+TimeStatsList = [os.path.join(args.pggbStats, file) for file in os.listdir(args.pggbStats) if file.split('.')[-2] == "time"]
+print(TimeStatsList)
+for pggbStats in TimeStatsList:
_tmpdf = pd.read_csv(
pggbStats,
@@ -101,7 +103,11 @@ for pggbStats in args.pggbStatsFiles:
# Getting Time, CPU and memory stats
time, cpu, memory = _tmpdf.iloc[4][1], int(_tmpdf.iloc[3][1][:-1]), int(_tmpdf.iloc[9][1])/((1024)**2)
- chrid = (os.path.basename(pggbStats)).split(".")[0]
+ chrid, stepName = (os.path.basename(pggbStats)).split(".")[:2]
+ stepName = stepName.replace("_", ".")
+
+ # Adding steps to identified pggb steps
+ if not stepName in PGGBsteps: PGGBsteps.append(stepName)
# Convert time to pd.timedelta (handling the 2 input types)
try :
@@ -109,10 +115,15 @@ for pggbStats in args.pggbStatsFiles:
except :
time = pd.to_timedelta(f"00:{time}")
- if args.debug: print(f"[timeStats::debug] Pangenome Name: {args.panname}\tChr: {chrid}\tTime: {time}\tCPU: {cpu}%\t memory: {memory}Gb")
+ if args.debug: print(f"[timeStats::debug] Pangenome Name: {args.panname}\tChr: {chrid}\tStep: {stepName}\tTime: {time}\tCPU: {cpu}%\t memory: {memory}Gb")
# Adding to aggregatedData
- aggregatedData[(args.panname, chrid)] = {"pggb.time": time, "pggb.cpu": cpu, "pggb.mem": memory}
+ if (args.panname, chrid) not in aggregatedData.keys():
+ aggregatedData[(args.panname, chrid)] = {f"{stepName}.time": time, f"{stepName}.cpu": cpu, f"{stepName}.mem": memory}
+ else :
+ aggregatedData[(args.panname, chrid)][f"{stepName}.time"] = time
+ aggregatedData[(args.panname, chrid)][f"{stepName}.cpu"] = cpu
+ aggregatedData[(args.panname, chrid)][f"{stepName}.mem"] = memory
## Parsing chromosome input file size (in #bases).
# Iterating over input length files
@@ -157,9 +168,13 @@ for graphStats in args.chrGraphStatsFiles:
df = pd.DataFrame.from_dict(aggregatedData, orient='index')
df.reset_index(inplace=True)
df.rename(columns={'level_0': 'Pangenome.name', 'level_1': 'Chr.id'}, inplace=True)
-df["pggb.time"] = pd.to_timedelta(df["pggb.time"])
-df["pggb.mem"] = df["pggb.mem"].astype(float)
-df["pggb.cpu"] = df["pggb.cpu"].astype(int)
+
+if args.debug: print(df)
+
+for step in PGGBsteps:
+ df[f"{step}.time"] = pd.to_timedelta(df[f"{step}.time"])
+ df[f"{step}.mem"] = df[f"{step}.mem"].astype(float)
+ df[f"{step}.cpu"] = df[f"{step}.cpu"].astype(int)
df["input.total.length"] = df["input.total.length"].astype(int)
if args.debug: print("[timeStats::debug]", df.dtypes)
@@ -167,6 +182,8 @@ if args.debug: print("[timeStats::debug]", df.dtypes)
# Saving the dataframe
df.to_csv(args.output, sep='\t', index=False)
+## Deprecated functions that may be repurposed in another script
+"""
# Creating some figures
# Time versus base count
sns.regplot(x=df["input.total.length"], y=df["pggb.time"].dt.total_seconds(), line_kws={"color":"r","alpha":0.7,"lw":5})
@@ -203,3 +220,4 @@ plt.ylabel('Peak memory usage (GB)')
plt.annotate(equation, xy=(0.05, 0.95), xycoords='axes fraction', fontsize=12, color='red')
plt.savefig(os.path.join(args.figdir,"MemoryVSCpu.png"))
plt.close()
+"""
\ No newline at end of file
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 761955cd2b445ebd1e1ea60af93080f9550bc310..2d068542076294be5327637d28cb3ec3c365470e 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -51,8 +51,9 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
#Â Minimap2 genome vs genome alignment
apptainer run --app minimap2 $appdir/PanGeTools.sif \
- -ax asm5 --eqx ${asmList[i]} ${asmList[i + 1]} -t $threads | \
- apptainer run --app samtools $appdir/PanGeTools.sif sort -O BAM -@ $threads - > $wrkdir/$bamFile
+ -a -x asm5 -c --eqx ${asmList[i]} ${asmList[i + 1]} -t $threads > $wrkdir/$bamFile.sam
+ apptainer run --app samtools $appdir/PanGeTools.sif sort -O BAM -@ $threads $wrkdir/$bamFile.sam > $wrkdir/$bamFile
+ rm $wrkdir/$bamFile.sam
# Syri on previous alignment
apptainer run $appdir/pan1c-env.sif \
diff --git a/scripts/getTags.py b/scripts/getTags.py
index 778c7ef0ebaac988f645a2620dbf0a87624ef223..4a5a95ede17382d8c2afc4b703b30f5fa53d0cd8 100644
--- a/scripts/getTags.py
+++ b/scripts/getTags.py
@@ -1,7 +1,7 @@
"""
Tag list creation script for Pan1c workflow
-Returns a list of tags to ad at the top of the final gfa file as commented lines.
+Returns a list of tags to add at the top of the final gfa file as commented lines.
@author: alexis.mergez@inrae.fr
@version: 1.0
diff --git a/scripts/inputClustering.py b/scripts/inputClustering.py
index b3688bb4cbbf12ee3c5a9c8f09b068e020fceb4e..6284eb4946b7e742726714c8917ad148e818beae 100644
--- a/scripts/inputClustering.py
+++ b/scripts/inputClustering.py
@@ -52,6 +52,8 @@ def getChr(name):
## Main script
seqDict = {}
+if args.debug: print(args.fastafiles)
+
# Parsing fasta files
for filename in args.fastafiles: