[2024-01-24 12:37:37,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference
[2024-01-24 12:37:41,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,017] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ea5b75b-cbda-4da4-815e-95f31aa61854/GCF_017873215.1_ASM1787321v1_genomic.fna.gz | prodigal -d GCF_017873215.1_ASM1787321v1_genomic.fna/cds.fna -a GCF_017873215.1_ASM1787321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:47,713] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:47,713] [INFO] Task started: HMMsearch
[2024-01-24 12:37:47,713] [INFO] Running command: hmmsearch --tblout GCF_017873215.1_ASM1787321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference/reference_markers.hmm GCF_017873215.1_ASM1787321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:48,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:48,024] [INFO] Found 6/6 markers.
[2024-01-24 12:37:48,061] [INFO] Query marker FASTA was written to GCF_017873215.1_ASM1787321v1_genomic.fna/markers.fasta
[2024-01-24 12:37:48,061] [INFO] Task started: Blastn
[2024-01-24 12:37:48,061] [INFO] Running command: blastn -query GCF_017873215.1_ASM1787321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference/reference_markers.fasta -out GCF_017873215.1_ASM1787321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:48,627] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:48,632] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:48,632] [INFO] Target genome list was writen to GCF_017873215.1_ASM1787321v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:48,687] [INFO] Task started: fastANI
[2024-01-24 12:37:48,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea5b75b-cbda-4da4-815e-95f31aa61854/GCF_017873215.1_ASM1787321v1_genomic.fna.gz --refList GCF_017873215.1_ASM1787321v1_genomic.fna/target_genomes.txt --output GCF_017873215.1_ASM1787321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:04,059] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:04,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:04,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:04,074] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:04,074] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:04,074] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	100.0	1424	1426	95	conclusive
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	83.6574	960	1426	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	81.3089	563	1426	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	78.8964	451	1426	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	78.7768	422	1426	95	below_threshold
Clostridium tetani	strain=ATCC 19406	GCA_900167265.1	1513	1513	type	True	78.1235	346	1426	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.8597	329	1426	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	77.7723	359	1426	95	below_threshold
Clostridium cochlearium	strain=NCTC13027	GCA_900187165.1	1494	1494	type	True	77.753	326	1426	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	77.4053	268	1426	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	77.3422	332	1426	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	77.2964	341	1426	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	77.2505	250	1426	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.6297	161	1426	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	76.5598	226	1426	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.2224	120	1426	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.0176	233	1426	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	75.8165	126	1426	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	74.8995	90	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:04,076] [INFO] DFAST Taxonomy check result was written to GCF_017873215.1_ASM1787321v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:04,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:04,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:04,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference/checkm_data
[2024-01-24 12:38:04,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:04,131] [INFO] Task started: CheckM
[2024-01-24 12:38:04,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873215.1_ASM1787321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873215.1_ASM1787321v1_genomic.fna/checkm_input GCF_017873215.1_ASM1787321v1_genomic.fna/checkm_result
[2024-01-24 12:38:30,935] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:30,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:30,959] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:30,961] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:30,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873215.1_ASM1787321v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:30,962] [INFO] Task started: Blastn
[2024-01-24 12:38:30,963] [INFO] Running command: blastn -query GCF_017873215.1_ASM1787321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e206ee0-dc4c-438d-b60c-45c86c74f0b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873215.1_ASM1787321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:31,754] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:31,757] [INFO] Selected 19 target genomes.
[2024-01-24 12:38:31,758] [INFO] Target genome list was writen to GCF_017873215.1_ASM1787321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:31,779] [INFO] Task started: fastANI
[2024-01-24 12:38:31,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea5b75b-cbda-4da4-815e-95f31aa61854/GCF_017873215.1_ASM1787321v1_genomic.fna.gz --refList GCF_017873215.1_ASM1787321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873215.1_ASM1787321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:42,874] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:42,888] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:42,889] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_017873215.1	s__Clostridium_AO tetanomorphum	100.0	1424	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	99.85	99.71	0.98	0.97	5	conclusive
GCF_000619945.1	s__Clostridium_AO lundense	83.6502	961	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002995785.1	s__Clostridium_AO liquoris	81.3261	560	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626095.1	s__Clostridium_AS rectalis	78.8864	452	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918285.1	s__MSJ-11 sp018918285	78.7665	423	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900205925.1	s__Clostridium_AK peptidivorans	78.7246	332	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167265.1	s__Clostridium_G tetani	78.1131	347	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.11	96.49	0.94	0.90	43	-
GCF_012926525.1	s__Clostridium_AM sp012926525	77.8505	330	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020205.1	s__Clostridium_F sporogenes	77.754	363	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	-
GCF_900187165.1	s__Clostridium_G cochlearium	77.753	326	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.06	98.56	0.90	0.85	10	-
GCF_000968375.1	s__Clostridium_AM scatologenes	77.7471	328	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_001276215.1	s__Clostridium_F sp001276215	77.3083	307	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_002008345.1	s__Clostridium_F tepidum	76.9221	289	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_900091705.1	s__Clostridium_P mediterraneense	75.8157	126	1426	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:42,891] [INFO] GTDB search result was written to GCF_017873215.1_ASM1787321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:42,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:42,895] [INFO] DFAST_QC result json was written to GCF_017873215.1_ASM1787321v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:42,896] [INFO] DFAST_QC completed!
[2024-01-24 12:38:42,896] [INFO] Total running time: 0h1m5s