[2023-03-15 18:39:13,541] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:13,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:13,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference
[2023-03-15 18:39:15,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:15,265] [INFO] Task started: Prodigal
[2023-03-15 18:39:15,265] [INFO] Running command: cat /var/lib/cwl/stg3aefa188-1cb0-4bf4-a1ea-5eea8439e8b1/OceanDNA-b13575.fa | prodigal -d OceanDNA-b13575/cds.fna -a OceanDNA-b13575/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:26,145] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:26,145] [INFO] Task started: HMMsearch
[2023-03-15 18:39:26,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b13575/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference/reference_markers.hmm OceanDNA-b13575/protein.faa > /dev/null
[2023-03-15 18:39:26,348] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:26,349] [INFO] Found 6/6 markers.
[2023-03-15 18:39:26,369] [INFO] Query marker FASTA was written to OceanDNA-b13575/markers.fasta
[2023-03-15 18:39:26,370] [INFO] Task started: Blastn
[2023-03-15 18:39:26,370] [INFO] Running command: blastn -query OceanDNA-b13575/markers.fasta -db /var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference/reference_markers.fasta -out OceanDNA-b13575/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:26,956] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:26,957] [INFO] Selected 18 target genomes.
[2023-03-15 18:39:26,957] [INFO] Target genome list was writen to OceanDNA-b13575/target_genomes.txt
[2023-03-15 18:39:26,973] [INFO] Task started: fastANI
[2023-03-15 18:39:26,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aefa188-1cb0-4bf4-a1ea-5eea8439e8b1/OceanDNA-b13575.fa --refList OceanDNA-b13575/target_genomes.txt --output OceanDNA-b13575/fastani_result.tsv --threads 1
[2023-03-15 18:39:39,492] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:39,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:39,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:39,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:39,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:39,493] [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
--------------------------------------------------------------------------------
[2023-03-15 18:39:39,493] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13575/tc_result.tsv
[2023-03-15 18:39:39,493] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:39,493] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:39,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference/checkm_data
[2023-03-15 18:39:39,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:39,504] [INFO] Task started: CheckM
[2023-03-15 18:39:39,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13575/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13575/checkm_input OceanDNA-b13575/checkm_result
[2023-03-15 18:40:11,520] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:11,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:11,523] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:11,523] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:11,523] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13575/markers.fasta)
[2023-03-15 18:40:11,525] [INFO] Task started: Blastn
[2023-03-15 18:40:11,525] [INFO] Running command: blastn -query OceanDNA-b13575/markers.fasta -db /var/lib/cwl/stg1a3d93f8-42f4-4a02-a4df-f03e87caaf9b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13575/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:12,490] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:12,491] [INFO] Selected 21 target genomes.
[2023-03-15 18:40:12,491] [INFO] Target genome list was writen to OceanDNA-b13575/target_genomes_gtdb.txt
[2023-03-15 18:40:13,220] [INFO] Task started: fastANI
[2023-03-15 18:40:13,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aefa188-1cb0-4bf4-a1ea-5eea8439e8b1/OceanDNA-b13575.fa --refList OceanDNA-b13575/target_genomes_gtdb.txt --output OceanDNA-b13575/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:25,577] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:25,581] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:40:25,582] [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_014382535.1	s__Desulfolinea nitratireducens	95.8328	481	575	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.72	99.72	0.90	0.90	2	conclusive
GCA_018648605.1	s__Desulfolinea sp018648605	77.6145	134	575	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.90	99.89	0.94	0.91	3	-
GCA_018645405.1	s__Desulfolinea sp018645405	77.3729	154	575	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.86	99.73	0.91	0.78	10	-
GCA_018648685.1	s__Desulfolinea sp018648685	77.1676	111	575	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.60	99.55	0.84	0.83	3	-
GCA_016744335.1	s__Desulfolinea sp016744335	76.8068	54	575	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648655.1	s__Desulfolinea sp018648655	76.5662	65	575	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.77	99.77	0.84	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:25,582] [INFO] GTDB search result was written to OceanDNA-b13575/result_gtdb.tsv
[2023-03-15 18:40:25,582] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:25,583] [INFO] DFAST_QC result json was written to OceanDNA-b13575/dqc_result.json
[2023-03-15 18:40:25,583] [INFO] DFAST_QC completed!
[2023-03-15 18:40:25,583] [INFO] Total running time: 0h1m12s