[2024-01-24 12:16:07,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:07,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:07,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference
[2024-01-24 12:16:08,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:08,537] [INFO] Task started: Prodigal
[2024-01-24 12:16:08,537] [INFO] Running command: gunzip -c /var/lib/cwl/stgc787d037-4269-4f07-9aea-1c9b33fe36cb/GCF_004015185.1_ASM401518v1_genomic.fna.gz | prodigal -d GCF_004015185.1_ASM401518v1_genomic.fna/cds.fna -a GCF_004015185.1_ASM401518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:19,020] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:19,021] [INFO] Task started: HMMsearch
[2024-01-24 12:16:19,021] [INFO] Running command: hmmsearch --tblout GCF_004015185.1_ASM401518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference/reference_markers.hmm GCF_004015185.1_ASM401518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:19,381] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:19,383] [INFO] Found 6/6 markers.
[2024-01-24 12:16:19,437] [INFO] Query marker FASTA was written to GCF_004015185.1_ASM401518v1_genomic.fna/markers.fasta
[2024-01-24 12:16:19,437] [INFO] Task started: Blastn
[2024-01-24 12:16:19,437] [INFO] Running command: blastn -query GCF_004015185.1_ASM401518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference/reference_markers.fasta -out GCF_004015185.1_ASM401518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,017] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,021] [INFO] Selected 23 target genomes.
[2024-01-24 12:16:20,021] [INFO] Target genome list was writen to GCF_004015185.1_ASM401518v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:20,028] [INFO] Task started: fastANI
[2024-01-24 12:16:20,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgc787d037-4269-4f07-9aea-1c9b33fe36cb/GCF_004015185.1_ASM401518v1_genomic.fna.gz --refList GCF_004015185.1_ASM401518v1_genomic.fna/target_genomes.txt --output GCF_004015185.1_ASM401518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:40,310] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:40,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:40,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:40,329] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:40,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:40,330] [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 manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	100.0	2121	2121	95	conclusive
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	81.2505	876	2121	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	80.9843	869	2121	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.5473	156	2121	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.9391	232	2121	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	77.9336	175	2121	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	77.5656	170	2121	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.5218	235	2121	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	77.4505	234	2121	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.9899	262	2121	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	76.808	177	2121	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	76.7881	204	2121	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.7562	168	2121	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.4308	164	2121	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	76.4249	156	2121	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.3888	169	2121	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.2367	148	2121	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.2366	111	2121	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	74.7971	50	2121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:40,332] [INFO] DFAST Taxonomy check result was written to GCF_004015185.1_ASM401518v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:40,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:40,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:40,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference/checkm_data
[2024-01-24 12:16:40,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:40,396] [INFO] Task started: CheckM
[2024-01-24 12:16:40,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004015185.1_ASM401518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004015185.1_ASM401518v1_genomic.fna/checkm_input GCF_004015185.1_ASM401518v1_genomic.fna/checkm_result
[2024-01-24 12:17:16,044] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:16,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:16,072] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:16,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:16,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004015185.1_ASM401518v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:16,073] [INFO] Task started: Blastn
[2024-01-24 12:17:16,074] [INFO] Running command: blastn -query GCF_004015185.1_ASM401518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg117c34e6-b860-43b4-b6f1-48e419e05a1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004015185.1_ASM401518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:16,848] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:16,852] [INFO] Selected 12 target genomes.
[2024-01-24 12:17:16,853] [INFO] Target genome list was writen to GCF_004015185.1_ASM401518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:16,861] [INFO] Task started: fastANI
[2024-01-24 12:17:16,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgc787d037-4269-4f07-9aea-1c9b33fe36cb/GCF_004015185.1_ASM401518v1_genomic.fna.gz --refList GCF_004015185.1_ASM401518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004015185.1_ASM401518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:30,250] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:30,262] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:30,263] [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_004015185.1	s__Clostridium_AR sp004015185	100.0	2121	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009928445.1	s__Clostridium_AR sp009928445	91.4991	1630	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193895.1	s__Clostridium_AR fungisolvens	81.1943	879	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017312485.1	s__Clostridium_AR sp017312485	80.9685	869	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595795.1	s__Clostridium_AR sp016595795	80.9615	852	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000619945.1	s__Clostridium_AO lundense	77.8862	176	2121	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_003606265.1	s__Clostridium septicum	77.747	178	2121	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_001403635.1	s__Clostridium_P massiliamazoniense	77.4142	170	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019207025.1	s__Clostridium_AM sp019207025	76.4659	164	2121	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_000320405.1	s__Clostridium celatum	76.4109	167	2121	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:30,264] [INFO] GTDB search result was written to GCF_004015185.1_ASM401518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:30,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:30,270] [INFO] DFAST_QC result json was written to GCF_004015185.1_ASM401518v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:30,270] [INFO] DFAST_QC completed!
[2024-01-24 12:17:30,270] [INFO] Total running time: 0h1m23s