[2023-03-17 04:15:14,761] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,761] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference
[2023-03-17 04:15:16,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,104] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,105] [INFO] Running command: cat /var/lib/cwl/stg455c1c44-9b8a-442e-a582-9b53e662cb08/OceanDNA-b34733.fa | prodigal -d OceanDNA-b34733/cds.fna -a OceanDNA-b34733/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:26,910] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:26,910] [INFO] Task started: HMMsearch
[2023-03-17 04:15:26,910] [INFO] Running command: hmmsearch --tblout OceanDNA-b34733/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference/reference_markers.hmm OceanDNA-b34733/protein.faa > /dev/null
[2023-03-17 04:15:27,120] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:27,121] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg455c1c44-9b8a-442e-a582-9b53e662cb08/OceanDNA-b34733.fa]
[2023-03-17 04:15:27,135] [INFO] Query marker FASTA was written to OceanDNA-b34733/markers.fasta
[2023-03-17 04:15:27,135] [INFO] Task started: Blastn
[2023-03-17 04:15:27,135] [INFO] Running command: blastn -query OceanDNA-b34733/markers.fasta -db /var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference/reference_markers.fasta -out OceanDNA-b34733/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:27,660] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:27,661] [INFO] Selected 19 target genomes.
[2023-03-17 04:15:27,661] [INFO] Target genome list was writen to OceanDNA-b34733/target_genomes.txt
[2023-03-17 04:15:27,671] [INFO] Task started: fastANI
[2023-03-17 04:15:27,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg455c1c44-9b8a-442e-a582-9b53e662cb08/OceanDNA-b34733.fa --refList OceanDNA-b34733/target_genomes.txt --output OceanDNA-b34733/fastani_result.tsv --threads 1
[2023-03-17 04:15:41,282] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:41,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:41,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:41,290] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:41,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:41,290] [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
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.1166	89	693	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.0468	115	693	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.0445	118	693	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	76.92	117	693	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	76.6891	109	693	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	76.6104	124	693	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	76.5657	87	693	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	76.4816	84	693	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	76.4744	89	693	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	76.4418	112	693	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:41,290] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34733/tc_result.tsv
[2023-03-17 04:15:41,290] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:41,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:41,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference/checkm_data
[2023-03-17 04:15:41,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:41,295] [INFO] Task started: CheckM
[2023-03-17 04:15:41,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34733/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34733/checkm_input OceanDNA-b34733/checkm_result
[2023-03-17 04:16:12,337] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:12,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:12,339] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:12,339] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:12,340] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34733/markers.fasta)
[2023-03-17 04:16:12,340] [INFO] Task started: Blastn
[2023-03-17 04:16:12,340] [INFO] Running command: blastn -query OceanDNA-b34733/markers.fasta -db /var/lib/cwl/stg68f0b9df-5c87-4098-89a3-b3249f4f76cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34733/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:13,015] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:13,016] [INFO] Selected 17 target genomes.
[2023-03-17 04:16:13,016] [INFO] Target genome list was writen to OceanDNA-b34733/target_genomes_gtdb.txt
[2023-03-17 04:16:13,105] [INFO] Task started: fastANI
[2023-03-17 04:16:13,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg455c1c44-9b8a-442e-a582-9b53e662cb08/OceanDNA-b34733.fa --refList OceanDNA-b34733/target_genomes_gtdb.txt --output OceanDNA-b34733/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:25,355] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:25,367] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:25,367] [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_018860755.1	s__Colwellia sp018860755	77.3254	122	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.2415	116	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	77.1579	126	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	77.1035	140	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	77.1007	112	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCF_005885605.1	s__Colwellia ponticola	77.0468	115	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843355.2	s__Colwellia echini	77.0445	118	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860915.1	s__Colwellia sp018860915	77.0392	138	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	76.9347	119	693	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	76.9224	120	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	76.8824	121	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	76.8433	106	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	76.8376	130	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCA_013214175.1	s__Colwellia sp013214175	76.8262	111	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	76.7464	89	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440345.1	s__Colwellia sp001440345	76.7159	105	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	76.5402	88	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:25,368] [INFO] GTDB search result was written to OceanDNA-b34733/result_gtdb.tsv
[2023-03-17 04:16:25,385] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:25,388] [INFO] DFAST_QC result json was written to OceanDNA-b34733/dqc_result.json
[2023-03-17 04:16:25,388] [INFO] DFAST_QC completed!
[2023-03-17 04:16:25,388] [INFO] Total running time: 0h1m11s