[2024-01-24 10:47:06,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg711687b2-2af6-4713-8dc2-ea5d99b271d9/GCF_002327185.1_ASM232718v1_genomic.fna.gz | prodigal -d GCF_002327185.1_ASM232718v1_genomic.fna/cds.fna -a GCF_002327185.1_ASM232718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:16,171] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:16,172] [INFO] Task started: HMMsearch
[2024-01-24 10:47:16,172] [INFO] Running command: hmmsearch --tblout GCF_002327185.1_ASM232718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference/reference_markers.hmm GCF_002327185.1_ASM232718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:16,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:16,600] [INFO] Found 6/6 markers.
[2024-01-24 10:47:16,632] [INFO] Query marker FASTA was written to GCF_002327185.1_ASM232718v1_genomic.fna/markers.fasta
[2024-01-24 10:47:16,652] [INFO] Task started: Blastn
[2024-01-24 10:47:16,652] [INFO] Running command: blastn -query GCF_002327185.1_ASM232718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference/reference_markers.fasta -out GCF_002327185.1_ASM232718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,631] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,634] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:19,635] [INFO] Target genome list was writen to GCF_002327185.1_ASM232718v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:19,755] [INFO] Task started: fastANI
[2024-01-24 10:47:19,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg711687b2-2af6-4713-8dc2-ea5d99b271d9/GCF_002327185.1_ASM232718v1_genomic.fna.gz --refList GCF_002327185.1_ASM232718v1_genomic.fna/target_genomes.txt --output GCF_002327185.1_ASM232718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:37,341] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:37,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:37,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:37,360] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:37,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:37,360] [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 chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	100.0	957	957	95	conclusive
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	85.4619	747	957	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	85.3622	753	957	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	79.4817	403	957	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	79.3814	420	957	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	79.0642	397	957	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	78.6434	391	957	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	78.3377	312	957	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	78.2834	312	957	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	78.2123	258	957	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	78.0749	296	957	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	78.05	246	957	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.0278	302	957	95	below_threshold
Peptacetobacter hiranonis	strain=DSM 13275	GCA_008151785.1	89152	89152	type	True	77.9133	59	957	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.8311	249	957	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.7453	238	957	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.5386	255	957	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	77.3625	240	957	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	76.9498	118	957	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	75.8809	125	957	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.0416	78	957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:37,362] [INFO] DFAST Taxonomy check result was written to GCF_002327185.1_ASM232718v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:37,362] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:37,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:37,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference/checkm_data
[2024-01-24 10:47:37,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:37,393] [INFO] Task started: CheckM
[2024-01-24 10:47:37,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002327185.1_ASM232718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002327185.1_ASM232718v1_genomic.fna/checkm_input GCF_002327185.1_ASM232718v1_genomic.fna/checkm_result
[2024-01-24 10:47:57,897] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:57,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,927] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:57,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:57,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002327185.1_ASM232718v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:57,928] [INFO] Task started: Blastn
[2024-01-24 10:47:57,928] [INFO] Running command: blastn -query GCF_002327185.1_ASM232718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb7aba7c-7026-46f5-b3ac-5d4a70b00727/dqc_reference/reference_markers_gtdb.fasta -out GCF_002327185.1_ASM232718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:58,873] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:58,876] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:58,877] [INFO] Target genome list was writen to GCF_002327185.1_ASM232718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:58,909] [INFO] Task started: fastANI
[2024-01-24 10:47:58,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg711687b2-2af6-4713-8dc2-ea5d99b271d9/GCF_002327185.1_ASM232718v1_genomic.fna.gz --refList GCF_002327185.1_ASM232718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002327185.1_ASM232718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:12,474] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:12,489] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:12,489] [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_002327185.1	s__Clostridium chauvoei	100.0	957	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	conclusive
GCF_003606265.1	s__Clostridium septicum	85.4329	746	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_015550425.1	s__Clostridium sp015550425	79.613	422	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCF_000401215.1	s__Clostridium sartagoforme_A	79.368	386	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCF_017873245.1	s__Clostridium tertium	79.3537	423	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCA_017888565.1	s__Clostridium sp017888565	79.1782	415	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794105.1	s__Clostridium sartagoforme_B	79.1241	374	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCF_014836325.1	s__Clostridium sp014836325	79.048	399	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759995.1	s__Clostridium sp900759995	79.0442	345	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCA_017435645.1	s__Clostridium sp017435645	78.766	189	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104115.1	s__Clostridium gasigenes	78.6533	390	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.21	97.55	0.90	0.87	10	-
GCA_018372555.1	s__Clostridium sp018372555	78.5985	291	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287815.1	s__Clostridium sp001916075	78.4648	244	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.32	99.07	0.94	0.92	6	-
GCF_015670405.1	s__Clostridium sp015670405	78.4532	306	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753455.2	s__Clostridium sp000753455	78.439	306	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.13	99.13	0.91	0.91	2	-
GCF_001405015.1	s__Clostridium disporicum	78.1595	303	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCA_003129525.1	s__Clostridium beijerinckii_D	78.139	246	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018372875.1	s__Clostridium sp018372875	78.0518	238	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCF_900129815.1	s__Asaccharospora irregularis	75.7066	69	957	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Asaccharospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,491] [INFO] GTDB search result was written to GCF_002327185.1_ASM232718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:12,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:12,495] [INFO] DFAST_QC result json was written to GCF_002327185.1_ASM232718v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:12,496] [INFO] DFAST_QC completed!
[2024-01-24 10:48:12,496] [INFO] Total running time: 0h1m6s