[2024-01-25 19:59:20,595] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:20,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:20,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference
[2024-01-25 19:59:21,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:21,716] [INFO] Task started: Prodigal
[2024-01-25 19:59:21,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ec989f8-3a27-434e-b400-732c8054728e/GCF_030409675.1_ASM3040967v1_genomic.fna.gz | prodigal -d GCF_030409675.1_ASM3040967v1_genomic.fna/cds.fna -a GCF_030409675.1_ASM3040967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:47,582] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:47,582] [INFO] Task started: HMMsearch
[2024-01-25 19:59:47,582] [INFO] Running command: hmmsearch --tblout GCF_030409675.1_ASM3040967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference/reference_markers.hmm GCF_030409675.1_ASM3040967v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:47,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:47,824] [INFO] Found 6/6 markers.
[2024-01-25 19:59:47,864] [INFO] Query marker FASTA was written to GCF_030409675.1_ASM3040967v1_genomic.fna/markers.fasta
[2024-01-25 19:59:47,864] [INFO] Task started: Blastn
[2024-01-25 19:59:47,865] [INFO] Running command: blastn -query GCF_030409675.1_ASM3040967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference/reference_markers.fasta -out GCF_030409675.1_ASM3040967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:48,419] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:48,422] [INFO] Selected 15 target genomes.
[2024-01-25 19:59:48,423] [INFO] Target genome list was writen to GCF_030409675.1_ASM3040967v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:48,447] [INFO] Task started: fastANI
[2024-01-25 19:59:48,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec989f8-3a27-434e-b400-732c8054728e/GCF_030409675.1_ASM3040967v1_genomic.fna.gz --refList GCF_030409675.1_ASM3040967v1_genomic.fna/target_genomes.txt --output GCF_030409675.1_ASM3040967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:01,844] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:01,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:01,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:01,852] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:01,852] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:01,853] [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
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	99.9941	1811	1821	95	conclusive
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	77.5722	364	1821	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	77.5716	356	1821	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	77.136	282	1821	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	76.9455	252	1821	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	76.7038	267	1821	95	below_threshold
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	76.5794	270	1821	95	below_threshold
Neolewinella aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	76.573	294	1821	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.2429	58	1821	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	75.1202	70	1821	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:01,854] [INFO] DFAST Taxonomy check result was written to GCF_030409675.1_ASM3040967v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:01,854] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:01,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:01,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference/checkm_data
[2024-01-25 20:00:01,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:01,912] [INFO] Task started: CheckM
[2024-01-25 20:00:01,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409675.1_ASM3040967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409675.1_ASM3040967v1_genomic.fna/checkm_input GCF_030409675.1_ASM3040967v1_genomic.fna/checkm_result
[2024-01-25 20:01:09,365] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:09,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:09,382] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:09,382] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:09,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409675.1_ASM3040967v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:09,383] [INFO] Task started: Blastn
[2024-01-25 20:01:09,383] [INFO] Running command: blastn -query GCF_030409675.1_ASM3040967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89125120-95a0-4e19-b045-b483b3b076b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409675.1_ASM3040967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:10,249] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:10,251] [INFO] Selected 15 target genomes.
[2024-01-25 20:01:10,251] [INFO] Target genome list was writen to GCF_030409675.1_ASM3040967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:10,263] [INFO] Task started: fastANI
[2024-01-25 20:01:10,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec989f8-3a27-434e-b400-732c8054728e/GCF_030409675.1_ASM3040967v1_genomic.fna.gz --refList GCF_030409675.1_ASM3040967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409675.1_ASM3040967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:26,631] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:26,639] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:26,639] [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_014349155.1	s__Lewinella_A lacunae	99.9941	1811	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002631205.1	s__Lewinella_A marina	77.5716	356	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803465.1	s__Lewinella_A litorea	77.1282	283	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004375085.3	s__Lewinella_A sp004375085	77.0204	372	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	76.9853	352	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197245.1	s__Lewinella_A aquimaris	76.9455	252	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625015.1	s__Lewinella_A sp001625015	76.8395	274	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390935.1	s__Lewinella_A sp003390935	76.7486	227	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373105.1	s__Lewinella_A persica	76.6637	313	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927835.1	s__Lewinella_A antarctica	76.5712	271	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014675.1	s__Lewinella_A aurantiaca	76.5675	292	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490175.1	s__WFYJ01 sp015490175	75.7334	76	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714985.1	s__UBA6168 sp016714985	75.3778	50	1821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA6168	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:26,641] [INFO] GTDB search result was written to GCF_030409675.1_ASM3040967v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:26,641] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:26,644] [INFO] DFAST_QC result json was written to GCF_030409675.1_ASM3040967v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:26,644] [INFO] DFAST_QC completed!
[2024-01-25 20:01:26,644] [INFO] Total running time: 0h2m6s