[2023-06-19 08:29:09,770] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:29:09,772] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:29:09,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference
[2023-06-19 08:29:11,151] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:29:11,154] [INFO] Task started: Prodigal
[2023-06-19 08:29:11,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg679c2ed5-da2b-498a-88de-457babd9e10f/GCA_013216005.1_ASM1321600v1_genomic.fna.gz | prodigal -d GCA_013216005.1_ASM1321600v1_genomic.fna/cds.fna -a GCA_013216005.1_ASM1321600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:29:19,432] [INFO] Task succeeded: Prodigal
[2023-06-19 08:29:19,432] [INFO] Task started: HMMsearch
[2023-06-19 08:29:19,433] [INFO] Running command: hmmsearch --tblout GCA_013216005.1_ASM1321600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference/reference_markers.hmm GCA_013216005.1_ASM1321600v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:29:19,768] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:29:19,769] [INFO] Found 6/6 markers.
[2023-06-19 08:29:19,810] [INFO] Query marker FASTA was written to GCA_013216005.1_ASM1321600v1_genomic.fna/markers.fasta
[2023-06-19 08:29:19,810] [INFO] Task started: Blastn
[2023-06-19 08:29:19,811] [INFO] Running command: blastn -query GCA_013216005.1_ASM1321600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference/reference_markers.fasta -out GCA_013216005.1_ASM1321600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:20,551] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:20,556] [INFO] Selected 21 target genomes.
[2023-06-19 08:29:20,556] [INFO] Target genome list was writen to GCA_013216005.1_ASM1321600v1_genomic.fna/target_genomes.txt
[2023-06-19 08:29:20,559] [INFO] Task started: fastANI
[2023-06-19 08:29:20,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg679c2ed5-da2b-498a-88de-457babd9e10f/GCA_013216005.1_ASM1321600v1_genomic.fna.gz --refList GCA_013216005.1_ASM1321600v1_genomic.fna/target_genomes.txt --output GCA_013216005.1_ASM1321600v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:29:34,211] [INFO] Task succeeded: fastANI
[2023-06-19 08:29:34,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:29:34,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:29:34,225] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:29:34,225] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:29:34,225] [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
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.555	157	1237	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.5149	177	1237	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.4874	193	1237	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4421	182	1237	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.3985	151	1237	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.3825	152	1237	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.3265	199	1237	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.2579	206	1237	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.1983	170	1237	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.1977	156	1237	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.0525	149	1237	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	76.5364	76	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:29:34,228] [INFO] DFAST Taxonomy check result was written to GCA_013216005.1_ASM1321600v1_genomic.fna/tc_result.tsv
[2023-06-19 08:29:34,229] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:29:34,230] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:29:34,230] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference/checkm_data
[2023-06-19 08:29:34,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:29:34,289] [INFO] Task started: CheckM
[2023-06-19 08:29:34,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013216005.1_ASM1321600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013216005.1_ASM1321600v1_genomic.fna/checkm_input GCA_013216005.1_ASM1321600v1_genomic.fna/checkm_result
[2023-06-19 08:30:05,792] [INFO] Task succeeded: CheckM
[2023-06-19 08:30:05,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 08:30:05,824] [INFO] ===== Completeness check finished =====
[2023-06-19 08:30:05,824] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:30:05,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013216005.1_ASM1321600v1_genomic.fna/markers.fasta)
[2023-06-19 08:30:05,825] [INFO] Task started: Blastn
[2023-06-19 08:30:05,825] [INFO] Running command: blastn -query GCA_013216005.1_ASM1321600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg026eb00c-d283-41a6-907d-301e4c31039a/dqc_reference/reference_markers_gtdb.fasta -out GCA_013216005.1_ASM1321600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:30:06,761] [INFO] Task succeeded: Blastn
[2023-06-19 08:30:06,766] [INFO] Selected 20 target genomes.
[2023-06-19 08:30:06,766] [INFO] Target genome list was writen to GCA_013216005.1_ASM1321600v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:30:06,773] [INFO] Task started: fastANI
[2023-06-19 08:30:06,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg679c2ed5-da2b-498a-88de-457babd9e10f/GCA_013216005.1_ASM1321600v1_genomic.fna.gz --refList GCA_013216005.1_ASM1321600v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013216005.1_ASM1321600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:30:24,215] [INFO] Task succeeded: fastANI
[2023-06-19 08:30:24,232] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:30:24,232] [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
GCA_013216005.1	s__JABSOI01 sp013216005	100.0	1218	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013216015.1	s__JABSOI01 sp013216015	85.8219	861	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	78.06	183	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215295.1	s__Colwellia_A sp013215295	77.7908	219	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001767295.1	s__Colwellia_A sp001767295	77.7194	194	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_018860755.1	s__Colwellia sp018860755	77.641	157	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.6296	176	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.6076	181	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	77.5868	185	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.5778	195	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_002843355.2	s__Colwellia echini	77.555	157	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	77.519	193	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_003545765.1	s__Litorilituus sp003545765	77.506	152	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.4367	237	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765535.1	s__GCA-2401725 sp016765535	77.4355	150	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	77.3985	151	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	77.367	179	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	77.3605	177	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	77.3291	198	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	77.2149	154	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:30:24,236] [INFO] GTDB search result was written to GCA_013216005.1_ASM1321600v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:30:24,237] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:30:24,241] [INFO] DFAST_QC result json was written to GCA_013216005.1_ASM1321600v1_genomic.fna/dqc_result.json
[2023-06-19 08:30:24,242] [INFO] DFAST_QC completed!
[2023-06-19 08:30:24,242] [INFO] Total running time: 0h1m14s