[2023-03-19 00:33:19,061] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,061] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference
[2023-03-19 00:33:20,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,315] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,315] [INFO] Running command: cat /var/lib/cwl/stg2fc047d4-5a6b-43de-9179-8af10d4027a4/OceanDNA-b46921.fa | prodigal -d OceanDNA-b46921/cds.fna -a OceanDNA-b46921/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:34:04,571] [INFO] Task succeeded: Prodigal
[2023-03-19 00:34:04,571] [INFO] Task started: HMMsearch
[2023-03-19 00:34:04,571] [INFO] Running command: hmmsearch --tblout OceanDNA-b46921/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference/reference_markers.hmm OceanDNA-b46921/protein.faa > /dev/null
[2023-03-19 00:34:04,879] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:34:04,879] [INFO] Found 6/6 markers.
[2023-03-19 00:34:04,915] [INFO] Query marker FASTA was written to OceanDNA-b46921/markers.fasta
[2023-03-19 00:34:04,917] [INFO] Task started: Blastn
[2023-03-19 00:34:04,917] [INFO] Running command: blastn -query OceanDNA-b46921/markers.fasta -db /var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference/reference_markers.fasta -out OceanDNA-b46921/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:08,371] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:08,373] [INFO] Selected 12 target genomes.
[2023-03-19 00:34:08,374] [INFO] Target genome list was writen to OceanDNA-b46921/target_genomes.txt
[2023-03-19 00:34:08,383] [INFO] Task started: fastANI
[2023-03-19 00:34:08,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc047d4-5a6b-43de-9179-8af10d4027a4/OceanDNA-b46921.fa --refList OceanDNA-b46921/target_genomes.txt --output OceanDNA-b46921/fastani_result.tsv --threads 1
[2023-03-19 00:34:18,274] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:18,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:34:18,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:34:18,275] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:34:18,275] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:34:18,275] [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
--------------------------------------------------------------------------------
[2023-03-19 00:34:18,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46921/tc_result.tsv
[2023-03-19 00:34:18,278] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:34:18,278] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:34:18,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference/checkm_data
[2023-03-19 00:34:18,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:34:18,289] [INFO] Task started: CheckM
[2023-03-19 00:34:18,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46921/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46921/checkm_input OceanDNA-b46921/checkm_result
[2023-03-19 00:36:05,842] [INFO] Task succeeded: CheckM
[2023-03-19 00:36:05,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:36:05,851] [INFO] ===== Completeness check finished =====
[2023-03-19 00:36:05,851] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:36:05,851] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46921/markers.fasta)
[2023-03-19 00:36:05,852] [INFO] Task started: Blastn
[2023-03-19 00:36:05,853] [INFO] Running command: blastn -query OceanDNA-b46921/markers.fasta -db /var/lib/cwl/stg87de5081-1f98-4780-a0ff-d523540544ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46921/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:36:06,530] [INFO] Task succeeded: Blastn
[2023-03-19 00:36:06,533] [INFO] Selected 20 target genomes.
[2023-03-19 00:36:06,534] [INFO] Target genome list was writen to OceanDNA-b46921/target_genomes_gtdb.txt
[2023-03-19 00:36:06,618] [INFO] Task started: fastANI
[2023-03-19 00:36:06,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc047d4-5a6b-43de-9179-8af10d4027a4/OceanDNA-b46921.fa --refList OceanDNA-b46921/target_genomes_gtdb.txt --output OceanDNA-b46921/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:36:19,513] [INFO] Task succeeded: fastANI
[2023-03-19 00:36:19,520] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:36:19,520] [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_013213905.1	s__Arctic95D-9 sp013213905	76.8772	250	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862135.1	s__Arctic95D-9 sp002862135	76.5957	148	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726915.1	s__Arctic95D-9 sp002726915	76.5524	121	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	99.85	99.85	0.91	0.91	2	-
GCA_002698785.1	s__Arctic95D-9 sp002698785	76.1153	115	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422425.1	s__Arctic95D-9 sp002422425	76.1064	91	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058245.1	s__Arctic95D-9 sp018058245	75.9382	75	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	99.34	99.34	0.85	0.85	2	-
GCA_002344215.1	s__Arctic95D-9 sp002344215	75.9146	100	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	75.8889	94	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344525.1	s__Arctic95D-9 sp002344525	75.833	71	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991025.1	s__Arctic95D-9 sp017991025	75.744	61	1789	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:36:19,521] [INFO] GTDB search result was written to OceanDNA-b46921/result_gtdb.tsv
[2023-03-19 00:36:19,522] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:36:19,523] [INFO] DFAST_QC result json was written to OceanDNA-b46921/dqc_result.json
[2023-03-19 00:36:19,523] [INFO] DFAST_QC completed!
[2023-03-19 00:36:19,523] [INFO] Total running time: 0h3m0s