[2023-03-16 23:35:12,967] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference
[2023-03-16 23:35:14,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,099] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stg62d3deac-21d5-4ebc-a437-7252a0effa77/OceanDNA-b3976.fa | prodigal -d OceanDNA-b3976/cds.fna -a OceanDNA-b3976/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:51,051] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:51,051] [INFO] Task started: HMMsearch
[2023-03-16 23:35:51,051] [INFO] Running command: hmmsearch --tblout OceanDNA-b3976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference/reference_markers.hmm OceanDNA-b3976/protein.faa > /dev/null
[2023-03-16 23:35:51,291] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:51,291] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg62d3deac-21d5-4ebc-a437-7252a0effa77/OceanDNA-b3976.fa]
[2023-03-16 23:35:51,319] [INFO] Query marker FASTA was written to OceanDNA-b3976/markers.fasta
[2023-03-16 23:35:51,320] [INFO] Task started: Blastn
[2023-03-16 23:35:51,320] [INFO] Running command: blastn -query OceanDNA-b3976/markers.fasta -db /var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference/reference_markers.fasta -out OceanDNA-b3976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:51,857] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:51,858] [INFO] Selected 10 target genomes.
[2023-03-16 23:35:51,858] [INFO] Target genome list was writen to OceanDNA-b3976/target_genomes.txt
[2023-03-16 23:35:51,864] [INFO] Task started: fastANI
[2023-03-16 23:35:51,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg62d3deac-21d5-4ebc-a437-7252a0effa77/OceanDNA-b3976.fa --refList OceanDNA-b3976/target_genomes.txt --output OceanDNA-b3976/fastani_result.tsv --threads 1
[2023-03-16 23:36:00,929] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:00,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:36:00,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:36:00,936] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:36:00,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:36:00,936] [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
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	82.4926	990	1712	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	81.5597	976	1712	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	81.1161	908	1712	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	80.9718	859	1712	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	80.4715	813	1712	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	80.4466	813	1712	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.2026	236	1712	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.1464	230	1712	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:36:00,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3976/tc_result.tsv
[2023-03-16 23:36:00,936] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:36:00,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:36:00,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference/checkm_data
[2023-03-16 23:36:00,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:36:00,944] [INFO] Task started: CheckM
[2023-03-16 23:36:00,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3976/checkm_input OceanDNA-b3976/checkm_result
[2023-03-16 23:37:31,674] [INFO] Task succeeded: CheckM
[2023-03-16 23:37:31,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:37:31,677] [INFO] ===== Completeness check finished =====
[2023-03-16 23:37:31,677] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:37:31,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3976/markers.fasta)
[2023-03-16 23:37:31,679] [INFO] Task started: Blastn
[2023-03-16 23:37:31,679] [INFO] Running command: blastn -query OceanDNA-b3976/markers.fasta -db /var/lib/cwl/stg3b98c30c-370d-44f6-b3ee-06279c2dcbce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:37:32,408] [INFO] Task succeeded: Blastn
[2023-03-16 23:37:32,409] [INFO] Selected 9 target genomes.
[2023-03-16 23:37:32,409] [INFO] Target genome list was writen to OceanDNA-b3976/target_genomes_gtdb.txt
[2023-03-16 23:37:32,562] [INFO] Task started: fastANI
[2023-03-16 23:37:32,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg62d3deac-21d5-4ebc-a437-7252a0effa77/OceanDNA-b3976.fa --refList OceanDNA-b3976/target_genomes_gtdb.txt --output OceanDNA-b3976/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:37:42,175] [INFO] Task succeeded: fastANI
[2023-03-16 23:37:42,182] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:37:42,182] [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
GCF_003259505.1	s__Algoriphagus yeomjeoni	82.4926	990	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	81.5655	975	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	81.2291	878	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	81.1164	908	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	80.9647	859	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	80.4466	813	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014838715.1	s__Algoriphagus sp014838715	80.1428	774	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442615.1	s__Algoriphagus resistens	79.4737	741	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.1464	230	1712	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:37:42,183] [INFO] GTDB search result was written to OceanDNA-b3976/result_gtdb.tsv
[2023-03-16 23:37:42,184] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:37:42,186] [INFO] DFAST_QC result json was written to OceanDNA-b3976/dqc_result.json
[2023-03-16 23:37:42,187] [INFO] DFAST_QC completed!
[2023-03-16 23:37:42,187] [INFO] Total running time: 0h2m29s