[2023-03-18 22:08:46,358] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:08:46,358] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:08:46,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference
[2023-03-18 22:08:47,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:08:47,440] [INFO] Task started: Prodigal
[2023-03-18 22:08:47,441] [INFO] Running command: cat /var/lib/cwl/stg4b42183c-9002-45ac-ac4e-2abebd24b019/OceanDNA-b11963.fa | prodigal -d OceanDNA-b11963/cds.fna -a OceanDNA-b11963/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:09:09,334] [INFO] Task succeeded: Prodigal
[2023-03-18 22:09:09,335] [INFO] Task started: HMMsearch
[2023-03-18 22:09:09,335] [INFO] Running command: hmmsearch --tblout OceanDNA-b11963/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference/reference_markers.hmm OceanDNA-b11963/protein.faa > /dev/null
[2023-03-18 22:09:09,499] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:09:09,499] [INFO] Found 6/6 markers.
[2023-03-18 22:09:09,515] [INFO] Query marker FASTA was written to OceanDNA-b11963/markers.fasta
[2023-03-18 22:09:09,516] [INFO] Task started: Blastn
[2023-03-18 22:09:09,517] [INFO] Running command: blastn -query OceanDNA-b11963/markers.fasta -db /var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference/reference_markers.fasta -out OceanDNA-b11963/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:09:10,121] [INFO] Task succeeded: Blastn
[2023-03-18 22:09:10,122] [INFO] Selected 35 target genomes.
[2023-03-18 22:09:10,122] [INFO] Target genome list was writen to OceanDNA-b11963/target_genomes.txt
[2023-03-18 22:09:10,155] [INFO] Task started: fastANI
[2023-03-18 22:09:10,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b42183c-9002-45ac-ac4e-2abebd24b019/OceanDNA-b11963.fa --refList OceanDNA-b11963/target_genomes.txt --output OceanDNA-b11963/fastani_result.tsv --threads 1
[2023-03-18 22:09:34,705] [INFO] Task succeeded: fastANI
[2023-03-18 22:09:34,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:09:34,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:09:34,706] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:09:34,706] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:09:34,706] [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
--------------------------------------------------------------------------------
[2023-03-18 22:09:34,706] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11963/tc_result.tsv
[2023-03-18 22:09:34,706] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:09:34,706] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:09:34,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference/checkm_data
[2023-03-18 22:09:34,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:09:34,788] [INFO] Task started: CheckM
[2023-03-18 22:09:34,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11963/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11963/checkm_input OceanDNA-b11963/checkm_result
[2023-03-18 22:10:34,790] [INFO] Task succeeded: CheckM
[2023-03-18 22:10:34,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:10:34,800] [INFO] ===== Completeness check finished =====
[2023-03-18 22:10:34,800] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:10:34,800] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11963/markers.fasta)
[2023-03-18 22:10:34,801] [INFO] Task started: Blastn
[2023-03-18 22:10:34,801] [INFO] Running command: blastn -query OceanDNA-b11963/markers.fasta -db /var/lib/cwl/stg30189d12-b9fa-4b99-938d-726133b11cb2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11963/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:10:35,623] [INFO] Task succeeded: Blastn
[2023-03-18 22:10:35,624] [INFO] Selected 17 target genomes.
[2023-03-18 22:10:35,624] [INFO] Target genome list was writen to OceanDNA-b11963/target_genomes_gtdb.txt
[2023-03-18 22:10:35,641] [INFO] Task started: fastANI
[2023-03-18 22:10:35,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b42183c-9002-45ac-ac4e-2abebd24b019/OceanDNA-b11963.fa --refList OceanDNA-b11963/target_genomes_gtdb.txt --output OceanDNA-b11963/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:10:44,166] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:44,175] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:10:44,175] [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_002862785.1	s__UBA8752 sp002862785	83.9825	488	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522855.1	s__UBA8752 sp011522855	83.6392	391	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172485.2	s__UBA8752 sp002172485	82.1062	302	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780385.1	s__UBA8752 sp016780385	78.7169	229	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535565.1	s__UBA8752 sp902535565	78.6384	126	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389295.1	s__UBA8752 sp002389295	78.5729	280	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.36	99.34	0.83	0.82	3	-
GCA_905478795.1	s__UBA8752 sp905478795	77.717	188	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336475.1	s__UBA8752 sp002336475	77.666	190	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.51	99.51	0.88	0.88	2	-
GCA_002720375.1	s__UBA8752 sp002720375	77.4266	148	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267055.1	s__PHOS-HE28 sp018267055	76.7112	79	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863145.1	s__UBA11663 sp002863145	76.1766	68	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
GCA_016713875.1	s__PHOS-HE28 sp016713875	76.0631	71	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.66	99.38	0.97	0.94	4	-
GCA_016788485.1	s__PHOS-HE28 sp016788485	75.9159	65	677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:10:44,175] [INFO] GTDB search result was written to OceanDNA-b11963/result_gtdb.tsv
[2023-03-18 22:10:44,175] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:10:44,176] [INFO] DFAST_QC result json was written to OceanDNA-b11963/dqc_result.json
[2023-03-18 22:10:44,176] [INFO] DFAST_QC completed!
[2023-03-18 22:10:44,176] [INFO] Total running time: 0h1m58s