[2024-01-24 12:13:56,229] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:56,231] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:56,232] [INFO] DQC Reference Directory: /var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference
[2024-01-24 12:13:57,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,519] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,519] [INFO] Running command: gunzip -c /var/lib/cwl/stgc07c1c33-bb61-47e9-8a3e-c96b01cd4445/GCF_003259265.1_ASM325926v1_genomic.fna.gz | prodigal -d GCF_003259265.1_ASM325926v1_genomic.fna/cds.fna -a GCF_003259265.1_ASM325926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:18,182] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:18,182] [INFO] Task started: HMMsearch
[2024-01-24 12:14:18,182] [INFO] Running command: hmmsearch --tblout GCF_003259265.1_ASM325926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference/reference_markers.hmm GCF_003259265.1_ASM325926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:18,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:18,506] [INFO] Found 6/6 markers.
[2024-01-24 12:14:18,544] [INFO] Query marker FASTA was written to GCF_003259265.1_ASM325926v1_genomic.fna/markers.fasta
[2024-01-24 12:14:18,545] [INFO] Task started: Blastn
[2024-01-24 12:14:18,545] [INFO] Running command: blastn -query GCF_003259265.1_ASM325926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference/reference_markers.fasta -out GCF_003259265.1_ASM325926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:19,267] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:19,271] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:19,271] [INFO] Target genome list was writen to GCF_003259265.1_ASM325926v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:19,277] [INFO] Task started: fastANI
[2024-01-24 12:14:19,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07c1c33-bb61-47e9-8a3e-c96b01cd4445/GCF_003259265.1_ASM325926v1_genomic.fna.gz --refList GCF_003259265.1_ASM325926v1_genomic.fna/target_genomes.txt --output GCF_003259265.1_ASM325926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:31,326] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:31,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:31,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:31,339] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:31,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:31,339] [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
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	100.0	1450	1458	95	conclusive
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	99.9522	1391	1458	95	conclusive
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	79.8633	671	1458	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	79.8582	610	1458	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	79.8559	610	1458	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	79.6369	643	1458	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	79.5048	651	1458	95	below_threshold
Gelidibacter maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	79.2288	571	1458	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	77.2586	72	1458	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.07	144	1458	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.0324	148	1458	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0184	132	1458	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.0133	152	1458	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9046	117	1458	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.8724	144	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:31,341] [INFO] DFAST Taxonomy check result was written to GCF_003259265.1_ASM325926v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:31,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:31,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:31,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference/checkm_data
[2024-01-24 12:14:31,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:31,389] [INFO] Task started: CheckM
[2024-01-24 12:14:31,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259265.1_ASM325926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259265.1_ASM325926v1_genomic.fna/checkm_input GCF_003259265.1_ASM325926v1_genomic.fna/checkm_result
[2024-01-24 12:15:30,123] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:30,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:30,142] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:30,143] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:30,143] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259265.1_ASM325926v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:30,143] [INFO] Task started: Blastn
[2024-01-24 12:15:30,144] [INFO] Running command: blastn -query GCF_003259265.1_ASM325926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7e8bbfc-17c6-4c52-a3f6-59a3e4ca5cea/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259265.1_ASM325926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,068] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,072] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:31,072] [INFO] Target genome list was writen to GCF_003259265.1_ASM325926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:31,081] [INFO] Task started: fastANI
[2024-01-24 12:15:31,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07c1c33-bb61-47e9-8a3e-c96b01cd4445/GCF_003259265.1_ASM325926v1_genomic.fna.gz --refList GCF_003259265.1_ASM325926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259265.1_ASM325926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:40,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:40,407] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:40,407] [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_001678675.1	s__Gelidibacter algens	99.9522	1391	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	conclusive
GCF_016469035.1	s__Gelidibacter salicanalis_A	80.8634	725	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364975.1	s__Gelidibacter sediminis	79.8654	608	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997285.1	s__Gelidibacter salicanalis	79.8582	610	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115975.1	s__Gelidibacter gilvus	79.8472	673	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423005.1	s__Gelidibacter mesophilus	79.6199	645	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581925.1	s__Gelidibacter sp017581925	79.4992	650	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725055.1	s__Gelidibacter japonicus	79.1988	593	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426755.1	s__Aquaticitalea sp002426755	77.4902	294	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	77.0327	149	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	76.353	137	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:40,409] [INFO] GTDB search result was written to GCF_003259265.1_ASM325926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:40,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:40,415] [INFO] DFAST_QC result json was written to GCF_003259265.1_ASM325926v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:40,415] [INFO] DFAST_QC completed!
[2024-01-24 12:15:40,415] [INFO] Total running time: 0h1m44s