[2023-03-15 08:59:47,043] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,043] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference
[2023-03-15 08:59:48,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,156] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,156] [INFO] Running command: cat /var/lib/cwl/stgccbbf54b-079e-4047-9b3a-3a114a6e3825/OceanDNA-b34669.fa | prodigal -d OceanDNA-b34669/cds.fna -a OceanDNA-b34669/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:10,517] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:10,518] [INFO] Task started: HMMsearch
[2023-03-15 09:00:10,518] [INFO] Running command: hmmsearch --tblout OceanDNA-b34669/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference/reference_markers.hmm OceanDNA-b34669/protein.faa > /dev/null
[2023-03-15 09:00:10,759] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:10,760] [INFO] Found 6/6 markers.
[2023-03-15 09:00:10,786] [INFO] Query marker FASTA was written to OceanDNA-b34669/markers.fasta
[2023-03-15 09:00:10,786] [INFO] Task started: Blastn
[2023-03-15 09:00:10,786] [INFO] Running command: blastn -query OceanDNA-b34669/markers.fasta -db /var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference/reference_markers.fasta -out OceanDNA-b34669/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:11,424] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:11,425] [INFO] Selected 18 target genomes.
[2023-03-15 09:00:11,425] [INFO] Target genome list was writen to OceanDNA-b34669/target_genomes.txt
[2023-03-15 09:00:11,434] [INFO] Task started: fastANI
[2023-03-15 09:00:11,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgccbbf54b-079e-4047-9b3a-3a114a6e3825/OceanDNA-b34669.fa --refList OceanDNA-b34669/target_genomes.txt --output OceanDNA-b34669/fastani_result.tsv --threads 1
[2023-03-15 09:00:25,479] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:25,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:25,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:25,487] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:25,488] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:25,488] [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 piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	79.2987	374	1428	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	79.2166	375	1428	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.171	436	1428	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.4773	335	1428	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.0328	282	1428	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.0125	296	1428	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.9584	263	1428	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4055	216	1428	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.2444	181	1428	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.1641	180	1428	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	76.4208	50	1428	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	76.134	54	1428	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:25,488] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34669/tc_result.tsv
[2023-03-15 09:00:25,488] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:25,488] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:25,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference/checkm_data
[2023-03-15 09:00:25,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:25,495] [INFO] Task started: CheckM
[2023-03-15 09:00:25,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34669/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34669/checkm_input OceanDNA-b34669/checkm_result
[2023-03-15 09:01:20,917] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:20,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:01:20,920] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:20,920] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:20,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34669/markers.fasta)
[2023-03-15 09:01:20,920] [INFO] Task started: Blastn
[2023-03-15 09:01:20,921] [INFO] Running command: blastn -query OceanDNA-b34669/markers.fasta -db /var/lib/cwl/stg50347d4c-35fc-4247-a1df-6e08db842a8e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34669/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:21,942] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:21,943] [INFO] Selected 12 target genomes.
[2023-03-15 09:01:21,943] [INFO] Target genome list was writen to OceanDNA-b34669/target_genomes_gtdb.txt
[2023-03-15 09:01:21,957] [INFO] Task started: fastANI
[2023-03-15 09:01:21,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgccbbf54b-079e-4047-9b3a-3a114a6e3825/OceanDNA-b34669.fa --refList OceanDNA-b34669/target_genomes_gtdb.txt --output OceanDNA-b34669/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:32,643] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:32,650] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:01:32,650] [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_013215465.1	s__Colwellia sp013215465	99.99	1381	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	conclusive
GCA_002733765.1	s__Colwellia sp002733765	85.4506	855	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCF_003333305.1	s__Colwellia aromaticivorans	85.4333	783	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003521815.1	s__Colwellia sp003521815	83.6279	553	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162675.1	s__Colwellia sp002162675	79.3887	469	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	79.3194	390	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_000378625.1	s__Colwellia piezophila	79.2896	375	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002207865.1	s__Colwellia marinimaniae	79.2489	372	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCA_016765685.1	s__Colwellia sp016765685	78.9266	334	1428	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	78.9257	423	1428	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	78.8375	418	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104455.1	s__Cognaticolwellia chukchiensis	77.2286	182	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:32,651] [INFO] GTDB search result was written to OceanDNA-b34669/result_gtdb.tsv
[2023-03-15 09:01:32,651] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:32,652] [INFO] DFAST_QC result json was written to OceanDNA-b34669/dqc_result.json
[2023-03-15 09:01:32,652] [INFO] DFAST_QC completed!
[2023-03-15 09:01:32,652] [INFO] Total running time: 0h1m46s