[2024-01-24 14:39:00,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:00,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:00,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference
[2024-01-24 14:39:02,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:02,221] [INFO] Task started: Prodigal
[2024-01-24 14:39:02,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ca2d526-1188-4eb4-858e-9a2d64003695/GCF_003606265.1_ASM360626v1_genomic.fna.gz | prodigal -d GCF_003606265.1_ASM360626v1_genomic.fna/cds.fna -a GCF_003606265.1_ASM360626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:07,497] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:07,497] [INFO] Task started: HMMsearch
[2024-01-24 14:39:07,497] [INFO] Running command: hmmsearch --tblout GCF_003606265.1_ASM360626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference/reference_markers.hmm GCF_003606265.1_ASM360626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:07,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:07,804] [INFO] Found 6/6 markers.
[2024-01-24 14:39:07,835] [INFO] Query marker FASTA was written to GCF_003606265.1_ASM360626v1_genomic.fna/markers.fasta
[2024-01-24 14:39:07,836] [INFO] Task started: Blastn
[2024-01-24 14:39:07,836] [INFO] Running command: blastn -query GCF_003606265.1_ASM360626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference/reference_markers.fasta -out GCF_003606265.1_ASM360626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:08,485] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:08,489] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:08,489] [INFO] Target genome list was writen to GCF_003606265.1_ASM360626v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:08,515] [INFO] Task started: fastANI
[2024-01-24 14:39:08,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ca2d526-1188-4eb4-858e-9a2d64003695/GCF_003606265.1_ASM360626v1_genomic.fna.gz --refList GCF_003606265.1_ASM360626v1_genomic.fna/target_genomes.txt --output GCF_003606265.1_ASM360626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:26,157] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:26,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:26,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:26,172] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:26,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:26,173] [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 septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	100.0	1133	1134	95	conclusive
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	99.9944	1131	1134	95	conclusive
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	85.2045	772	1134	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	79.2673	444	1134	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	79.114	436	1134	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	78.9752	409	1134	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	78.6033	388	1134	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	78.2883	276	1134	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	78.0524	264	1134	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	78.0436	351	1134	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.9136	280	1134	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.7903	191	1134	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	77.6649	235	1134	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.5089	232	1134	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.4165	252	1134	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	77.2961	258	1134	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	77.2861	258	1134	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.4531	149	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:26,175] [INFO] DFAST Taxonomy check result was written to GCF_003606265.1_ASM360626v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:26,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:26,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:26,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference/checkm_data
[2024-01-24 14:39:26,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:26,215] [INFO] Task started: CheckM
[2024-01-24 14:39:26,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003606265.1_ASM360626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003606265.1_ASM360626v1_genomic.fna/checkm_input GCF_003606265.1_ASM360626v1_genomic.fna/checkm_result
[2024-01-24 14:39:49,576] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:49,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:49,602] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:49,603] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:49,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003606265.1_ASM360626v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:49,604] [INFO] Task started: Blastn
[2024-01-24 14:39:49,604] [INFO] Running command: blastn -query GCF_003606265.1_ASM360626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f679dc3-c963-4dc3-a17f-a6f0bbb65f9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003606265.1_ASM360626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:50,475] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:50,480] [INFO] Selected 17 target genomes.
[2024-01-24 14:39:50,481] [INFO] Target genome list was writen to GCF_003606265.1_ASM360626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:50,495] [INFO] Task started: fastANI
[2024-01-24 14:39:50,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ca2d526-1188-4eb4-858e-9a2d64003695/GCF_003606265.1_ASM360626v1_genomic.fna.gz --refList GCF_003606265.1_ASM360626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003606265.1_ASM360626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:04,005] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:04,020] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:04,020] [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_003606265.1	s__Clostridium septicum	100.0	1132	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	conclusive
GCF_002327185.1	s__Clostridium chauvoei	85.2085	775	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_017873245.1	s__Clostridium tertium	79.283	442	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_015550425.1	s__Clostridium sp015550425	79.1552	461	1134	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_900086595.1	s__Clostridium nigeriense	79.095	438	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.98	98.98	0.91	0.91	2	-
GCF_000401215.1	s__Clostridium sartagoforme_A	79.0257	404	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCA_017888565.1	s__Clostridium sp017888565	78.9976	449	1134	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_014836325.1	s__Clostridium sp014836325	78.9922	408	1134	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	78.8984	354	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCF_900104115.1	s__Clostridium gasigenes	78.6239	386	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.21	97.55	0.90	0.87	10	-
GCF_004794105.1	s__Clostridium sartagoforme_B	78.5386	388	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCA_018372555.1	s__Clostridium sp018372555	78.1849	309	1134	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_001405015.1	s__Clostridium disporicum	78.1725	308	1134	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_900547475.1	s__Clostridium sp900547475	78.1598	356	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_015667795.1	s__Clostridium sp015667795	78.0321	385	1134	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_900543325.1	s__Clostridium sp900543325	77.7066	320	1134	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_017383505.1	s__Clostridium sp017383505	77.619	182	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:04,022] [INFO] GTDB search result was written to GCF_003606265.1_ASM360626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:04,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:04,026] [INFO] DFAST_QC result json was written to GCF_003606265.1_ASM360626v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:04,027] [INFO] DFAST_QC completed!
[2024-01-24 14:40:04,027] [INFO] Total running time: 0h1m3s