[2024-01-24 12:16:08,001] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference
[2024-01-24 12:16:09,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,345] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg68ef6a10-7b2d-4eb5-9a85-3134a5016b38/GCF_014062315.1_ASM1406231v1_genomic.fna.gz | prodigal -d GCF_014062315.1_ASM1406231v1_genomic.fna/cds.fna -a GCF_014062315.1_ASM1406231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:29,477] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:29,478] [INFO] Task started: HMMsearch
[2024-01-24 12:16:29,478] [INFO] Running command: hmmsearch --tblout GCF_014062315.1_ASM1406231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference/reference_markers.hmm GCF_014062315.1_ASM1406231v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:29,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:29,770] [INFO] Found 6/6 markers.
[2024-01-24 12:16:29,811] [INFO] Query marker FASTA was written to GCF_014062315.1_ASM1406231v1_genomic.fna/markers.fasta
[2024-01-24 12:16:29,811] [INFO] Task started: Blastn
[2024-01-24 12:16:29,812] [INFO] Running command: blastn -query GCF_014062315.1_ASM1406231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference/reference_markers.fasta -out GCF_014062315.1_ASM1406231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:30,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:30,487] [INFO] Selected 14 target genomes.
[2024-01-24 12:16:30,487] [INFO] Target genome list was writen to GCF_014062315.1_ASM1406231v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:30,494] [INFO] Task started: fastANI
[2024-01-24 12:16:30,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg68ef6a10-7b2d-4eb5-9a85-3134a5016b38/GCF_014062315.1_ASM1406231v1_genomic.fna.gz --refList GCF_014062315.1_ASM1406231v1_genomic.fna/target_genomes.txt --output GCF_014062315.1_ASM1406231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:41,280] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:41,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:41,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:41,297] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:41,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:41,297] [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 maritimus	strain=F6074	GCA_014062315.1	2761487	2761487	type	True	100.0	1538	1543	95	conclusive
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	85.4041	1153	1543	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	84.3993	1072	1543	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	82.5403	1028	1543	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	79.9542	767	1543	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	78.9803	588	1543	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	78.6421	510	1543	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.1832	151	1543	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.8072	105	1543	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7444	141	1543	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.636	67	1543	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.6212	109	1543	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5299	127	1543	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.4906	123	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:41,299] [INFO] DFAST Taxonomy check result was written to GCF_014062315.1_ASM1406231v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:41,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:41,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:41,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference/checkm_data
[2024-01-24 12:16:41,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:41,351] [INFO] Task started: CheckM
[2024-01-24 12:16:41,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014062315.1_ASM1406231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014062315.1_ASM1406231v1_genomic.fna/checkm_input GCF_014062315.1_ASM1406231v1_genomic.fna/checkm_result
[2024-01-24 12:17:39,808] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:39,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:39,836] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:39,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:39,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014062315.1_ASM1406231v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:39,838] [INFO] Task started: Blastn
[2024-01-24 12:17:39,838] [INFO] Running command: blastn -query GCF_014062315.1_ASM1406231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05f8c88c-4d59-4bfb-a8b0-2dd26427749a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014062315.1_ASM1406231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:40,742] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:40,746] [INFO] Selected 9 target genomes.
[2024-01-24 12:17:40,746] [INFO] Target genome list was writen to GCF_014062315.1_ASM1406231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:40,748] [INFO] Task started: fastANI
[2024-01-24 12:17:40,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg68ef6a10-7b2d-4eb5-9a85-3134a5016b38/GCF_014062315.1_ASM1406231v1_genomic.fna.gz --refList GCF_014062315.1_ASM1406231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014062315.1_ASM1406231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:48,907] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:48,920] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:48,920] [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_014062315.1	s__Gelidibacter sp014062315	100.0	1538	1543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017581925.1	s__Gelidibacter sp017581925	85.4041	1153	1543	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	84.392	1074	1543	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	82.5403	1028	1543	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	79.9508	767	1543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678675.1	s__Gelidibacter algens	79.0732	565	1543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	99.95	99.95	0.98	0.98	2	-
GCF_004364975.1	s__Gelidibacter sediminis	78.6379	510	1543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.7378	151	1543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.4877	122	1543	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:48,922] [INFO] GTDB search result was written to GCF_014062315.1_ASM1406231v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:48,922] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:48,926] [INFO] DFAST_QC result json was written to GCF_014062315.1_ASM1406231v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:48,926] [INFO] DFAST_QC completed!
[2024-01-24 12:17:48,926] [INFO] Total running time: 0h1m41s