[2024-01-24 14:28:18,060] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:18,063] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:18,063] [INFO] DQC Reference Directory: /var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference
[2024-01-24 14:28:20,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:20,486] [INFO] Task started: Prodigal
[2024-01-24 14:28:20,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg056c617f-e9ea-4ada-9966-e62ec0060842/GCF_002749945.1_ASM274994v1_genomic.fna.gz | prodigal -d GCF_002749945.1_ASM274994v1_genomic.fna/cds.fna -a GCF_002749945.1_ASM274994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:26,458] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:26,459] [INFO] Task started: HMMsearch
[2024-01-24 14:28:26,459] [INFO] Running command: hmmsearch --tblout GCF_002749945.1_ASM274994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference/reference_markers.hmm GCF_002749945.1_ASM274994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:26,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:26,769] [INFO] Found 6/6 markers.
[2024-01-24 14:28:26,806] [INFO] Query marker FASTA was written to GCF_002749945.1_ASM274994v1_genomic.fna/markers.fasta
[2024-01-24 14:28:26,807] [INFO] Task started: Blastn
[2024-01-24 14:28:26,807] [INFO] Running command: blastn -query GCF_002749945.1_ASM274994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference/reference_markers.fasta -out GCF_002749945.1_ASM274994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:27,456] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:27,460] [INFO] Selected 15 target genomes.
[2024-01-24 14:28:27,460] [INFO] Target genome list was writen to GCF_002749945.1_ASM274994v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:27,467] [INFO] Task started: fastANI
[2024-01-24 14:28:27,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg056c617f-e9ea-4ada-9966-e62ec0060842/GCF_002749945.1_ASM274994v1_genomic.fna.gz --refList GCF_002749945.1_ASM274994v1_genomic.fna/target_genomes.txt --output GCF_002749945.1_ASM274994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:40,567] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:40,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:40,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:40,579] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:28:40,580] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:28:40,580] [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 combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	100.0	1278	1278	95	inconclusive
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	97.397	1161	1278	95	inconclusive
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	97.3445	1136	1278	95	inconclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	91.986	1090	1278	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	91.9706	1093	1278	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	78.2409	253	1278	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	77.7334	329	1278	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	77.4821	218	1278	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	76.5409	202	1278	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	76.4056	169	1278	95	below_threshold
Clostridium bornimense	strain=type strain: M2/40	GCA_000577895.1	1216932	1216932	type	True	76.0574	146	1278	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	76.042	172	1278	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	76.0416	172	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:40,582] [INFO] DFAST Taxonomy check result was written to GCF_002749945.1_ASM274994v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:40,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:40,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:40,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference/checkm_data
[2024-01-24 14:28:40,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:40,624] [INFO] Task started: CheckM
[2024-01-24 14:28:40,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002749945.1_ASM274994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002749945.1_ASM274994v1_genomic.fna/checkm_input GCF_002749945.1_ASM274994v1_genomic.fna/checkm_result
[2024-01-24 14:29:04,719] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:04,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:04,743] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:04,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:04,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002749945.1_ASM274994v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:04,745] [INFO] Task started: Blastn
[2024-01-24 14:29:04,745] [INFO] Running command: blastn -query GCF_002749945.1_ASM274994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca4dc0ca-d320-4eb5-9777-cb668c4b697a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002749945.1_ASM274994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:05,525] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:05,529] [INFO] Selected 5 target genomes.
[2024-01-24 14:29:05,530] [INFO] Target genome list was writen to GCF_002749945.1_ASM274994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:05,534] [INFO] Task started: fastANI
[2024-01-24 14:29:05,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg056c617f-e9ea-4ada-9966-e62ec0060842/GCF_002749945.1_ASM274994v1_genomic.fna.gz --refList GCF_002749945.1_ASM274994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002749945.1_ASM274994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:11,961] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:11,967] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:11,967] [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_001276985.1	s__Clostridium_F botulinum	97.4166	1160	1278	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	conclusive
GCF_001889325.1	s__Clostridium_F botulinum_A	93.4495	1129	1278	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_001020205.1	s__Clostridium_F sporogenes	91.9681	1094	1278	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_001276215.1	s__Clostridium_F sp001276215	89.2058	975	1278	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	87.9031	811	1278	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:11,969] [INFO] GTDB search result was written to GCF_002749945.1_ASM274994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:11,970] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:11,973] [INFO] DFAST_QC result json was written to GCF_002749945.1_ASM274994v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:11,973] [INFO] DFAST_QC completed!
[2024-01-24 14:29:11,974] [INFO] Total running time: 0h0m54s