[2023-03-17 01:01:12,724] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:01:12,724] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:01:12,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference
[2023-03-17 01:01:14,627] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:01:14,627] [INFO] Task started: Prodigal
[2023-03-17 01:01:14,627] [INFO] Running command: cat /var/lib/cwl/stg6f1bd87b-cee4-4b4b-8752-2ed3d4506cc4/OceanDNA-b34725.fa | prodigal -d OceanDNA-b34725/cds.fna -a OceanDNA-b34725/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:01:29,808] [INFO] Task succeeded: Prodigal
[2023-03-17 01:01:29,808] [INFO] Task started: HMMsearch
[2023-03-17 01:01:29,808] [INFO] Running command: hmmsearch --tblout OceanDNA-b34725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference/reference_markers.hmm OceanDNA-b34725/protein.faa > /dev/null
[2023-03-17 01:01:29,989] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:01:29,990] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6f1bd87b-cee4-4b4b-8752-2ed3d4506cc4/OceanDNA-b34725.fa]
[2023-03-17 01:01:30,014] [INFO] Query marker FASTA was written to OceanDNA-b34725/markers.fasta
[2023-03-17 01:01:30,014] [INFO] Task started: Blastn
[2023-03-17 01:01:30,014] [INFO] Running command: blastn -query OceanDNA-b34725/markers.fasta -db /var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference/reference_markers.fasta -out OceanDNA-b34725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:30,457] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:30,458] [INFO] Selected 16 target genomes.
[2023-03-17 01:01:30,458] [INFO] Target genome list was writen to OceanDNA-b34725/target_genomes.txt
[2023-03-17 01:01:30,466] [INFO] Task started: fastANI
[2023-03-17 01:01:30,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f1bd87b-cee4-4b4b-8752-2ed3d4506cc4/OceanDNA-b34725.fa --refList OceanDNA-b34725/target_genomes.txt --output OceanDNA-b34725/fastani_result.tsv --threads 1
[2023-03-17 01:01:42,169] [INFO] Task succeeded: fastANI
[2023-03-17 01:01:42,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:01:42,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:01:42,176] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:01:42,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:01:42,176] [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 hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	79.7855	422	974	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.3718	143	974	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.1946	176	974	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	77.0428	133	974	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	76.9192	118	974	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	76.8172	105	974	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.8119	137	974	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	76.7397	103	974	95	below_threshold
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	75.9771	71	974	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:01:42,176] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34725/tc_result.tsv
[2023-03-17 01:01:42,177] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:01:42,177] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:01:42,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference/checkm_data
[2023-03-17 01:01:42,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:01:42,230] [INFO] Task started: CheckM
[2023-03-17 01:01:42,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34725/checkm_input OceanDNA-b34725/checkm_result
[2023-03-17 01:02:22,417] [INFO] Task succeeded: CheckM
[2023-03-17 01:02:22,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:02:22,420] [INFO] ===== Completeness check finished =====
[2023-03-17 01:02:22,421] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:02:22,421] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34725/markers.fasta)
[2023-03-17 01:02:22,422] [INFO] Task started: Blastn
[2023-03-17 01:02:22,422] [INFO] Running command: blastn -query OceanDNA-b34725/markers.fasta -db /var/lib/cwl/stg12cee0c2-650e-4775-861c-d3906a845c32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:02:22,859] [INFO] Task succeeded: Blastn
[2023-03-17 01:02:22,860] [INFO] Selected 9 target genomes.
[2023-03-17 01:02:22,860] [INFO] Target genome list was writen to OceanDNA-b34725/target_genomes_gtdb.txt
[2023-03-17 01:02:22,998] [INFO] Task started: fastANI
[2023-03-17 01:02:22,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f1bd87b-cee4-4b4b-8752-2ed3d4506cc4/OceanDNA-b34725.fa --refList OceanDNA-b34725/target_genomes_gtdb.txt --output OceanDNA-b34725/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:02:31,052] [INFO] Task succeeded: fastANI
[2023-03-17 01:02:31,058] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:02:31,058] [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_013215385.1	s__Colwellia_A sp013215385	93.2604	913	974	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_013215295.1	s__Colwellia_A sp013215295	81.0636	539	974	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_007954355.1	s__Colwellia_A hornerae	79.777	421	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_014076845.1	s__Colwellia_A sp014076845	79.7041	434	974	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_001767295.1	s__Colwellia_A sp001767295	79.3856	417	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCA_013214175.1	s__Colwellia sp013214175	77.7693	148	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	77.1941	149	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	76.9622	153	974	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	76.9612	184	974	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 01:02:31,058] [INFO] GTDB search result was written to OceanDNA-b34725/result_gtdb.tsv
[2023-03-17 01:02:31,058] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:02:31,059] [INFO] DFAST_QC result json was written to OceanDNA-b34725/dqc_result.json
[2023-03-17 01:02:31,060] [INFO] DFAST_QC completed!
[2023-03-17 01:02:31,060] [INFO] Total running time: 0h1m18s