[2023-03-19 05:04:10,734] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:04:10,734] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:04:10,734] [INFO] DQC Reference Directory: /var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference
[2023-03-19 05:04:11,997] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:04:11,997] [INFO] Task started: Prodigal
[2023-03-19 05:04:11,997] [INFO] Running command: cat /var/lib/cwl/stg742e0be2-893f-4c6c-8fa7-ac840c2df9c8/OceanDNA-b20811.fa | prodigal -d OceanDNA-b20811/cds.fna -a OceanDNA-b20811/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:04:28,733] [INFO] Task succeeded: Prodigal
[2023-03-19 05:04:28,733] [INFO] Task started: HMMsearch
[2023-03-19 05:04:28,733] [INFO] Running command: hmmsearch --tblout OceanDNA-b20811/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference/reference_markers.hmm OceanDNA-b20811/protein.faa > /dev/null
[2023-03-19 05:04:28,912] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:04:28,912] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg742e0be2-893f-4c6c-8fa7-ac840c2df9c8/OceanDNA-b20811.fa]
[2023-03-19 05:04:28,930] [INFO] Query marker FASTA was written to OceanDNA-b20811/markers.fasta
[2023-03-19 05:04:28,931] [INFO] Task started: Blastn
[2023-03-19 05:04:28,931] [INFO] Running command: blastn -query OceanDNA-b20811/markers.fasta -db /var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference/reference_markers.fasta -out OceanDNA-b20811/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:04:29,421] [INFO] Task succeeded: Blastn
[2023-03-19 05:04:29,422] [INFO] Selected 18 target genomes.
[2023-03-19 05:04:29,422] [INFO] Target genome list was writen to OceanDNA-b20811/target_genomes.txt
[2023-03-19 05:04:29,452] [INFO] Task started: fastANI
[2023-03-19 05:04:29,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg742e0be2-893f-4c6c-8fa7-ac840c2df9c8/OceanDNA-b20811.fa --refList OceanDNA-b20811/target_genomes.txt --output OceanDNA-b20811/fastani_result.tsv --threads 1
[2023-03-19 05:04:41,595] [INFO] Task succeeded: fastANI
[2023-03-19 05:04:41,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:04:41,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:04:41,595] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:04:41,595] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:04:41,595] [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 05:04:41,596] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20811/tc_result.tsv
[2023-03-19 05:04:41,596] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:04:41,596] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:04:41,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference/checkm_data
[2023-03-19 05:04:41,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:04:41,602] [INFO] Task started: CheckM
[2023-03-19 05:04:41,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20811/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20811/checkm_input OceanDNA-b20811/checkm_result
[2023-03-19 05:05:26,100] [INFO] Task succeeded: CheckM
[2023-03-19 05:05:26,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:05:26,102] [INFO] ===== Completeness check finished =====
[2023-03-19 05:05:26,102] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:05:26,103] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20811/markers.fasta)
[2023-03-19 05:05:26,103] [INFO] Task started: Blastn
[2023-03-19 05:05:26,103] [INFO] Running command: blastn -query OceanDNA-b20811/markers.fasta -db /var/lib/cwl/stgbffdd61d-073e-4442-940d-53bf10b1a00f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20811/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:05:26,746] [INFO] Task succeeded: Blastn
[2023-03-19 05:05:26,746] [INFO] Selected 17 target genomes.
[2023-03-19 05:05:26,746] [INFO] Target genome list was writen to OceanDNA-b20811/target_genomes_gtdb.txt
[2023-03-19 05:05:26,856] [INFO] Task started: fastANI
[2023-03-19 05:05:26,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg742e0be2-893f-4c6c-8fa7-ac840c2df9c8/OceanDNA-b20811.fa --refList OceanDNA-b20811/target_genomes_gtdb.txt --output OceanDNA-b20811/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:05:37,152] [INFO] Task succeeded: fastANI
[2023-03-19 05:05:37,158] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:05:37,158] [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_018673925.1	s__JABMPR01 sp018673925	78.4652	272	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_016845065.1	s__JABMPR01 sp016845065	78.3948	255	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784025.1	s__JABMPR01 sp014382565	78.2842	257	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.96	99.93	0.94	0.93	3	-
GCA_016784545.1	s__JABMPR01 sp016784545	77.8745	254	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650795.1	s__JABMPR01 sp018650795	77.8523	218	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.79	99.56	0.89	0.81	14	-
GCA_018650445.1	s__JABMPR01 sp018650445	77.7239	233	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
GCA_013203185.1	s__JABMPR01 sp013203185	77.3811	217	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013202495.1	s__JABMPR01 sp013202495	77.2576	226	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013202895.1	s__JABMPR01 sp013202895	76.0546	55	961	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:05:37,158] [INFO] GTDB search result was written to OceanDNA-b20811/result_gtdb.tsv
[2023-03-19 05:05:37,158] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:05:37,159] [INFO] DFAST_QC result json was written to OceanDNA-b20811/dqc_result.json
[2023-03-19 05:05:37,159] [INFO] DFAST_QC completed!
[2023-03-19 05:05:37,159] [INFO] Total running time: 0h1m26s