[2023-03-15 17:24:01,288] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,289] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference
[2023-03-15 17:24:02,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,547] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,547] [INFO] Running command: cat /var/lib/cwl/stgd305bd27-dc63-4379-b6d2-efba21f8a127/OceanDNA-b8078.fa | prodigal -d OceanDNA-b8078/cds.fna -a OceanDNA-b8078/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:09,232] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:09,233] [INFO] Task started: HMMsearch
[2023-03-15 17:24:09,233] [INFO] Running command: hmmsearch --tblout OceanDNA-b8078/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference/reference_markers.hmm OceanDNA-b8078/protein.faa > /dev/null
[2023-03-15 17:24:09,495] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:09,496] [INFO] Found 6/6 markers.
[2023-03-15 17:24:09,505] [INFO] Query marker FASTA was written to OceanDNA-b8078/markers.fasta
[2023-03-15 17:24:09,505] [INFO] Task started: Blastn
[2023-03-15 17:24:09,505] [INFO] Running command: blastn -query OceanDNA-b8078/markers.fasta -db /var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference/reference_markers.fasta -out OceanDNA-b8078/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:10,115] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:10,116] [INFO] Selected 30 target genomes.
[2023-03-15 17:24:10,116] [INFO] Target genome list was writen to OceanDNA-b8078/target_genomes.txt
[2023-03-15 17:24:10,130] [INFO] Task started: fastANI
[2023-03-15 17:24:10,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgd305bd27-dc63-4379-b6d2-efba21f8a127/OceanDNA-b8078.fa --refList OceanDNA-b8078/target_genomes.txt --output OceanDNA-b8078/fastani_result.tsv --threads 1
[2023-03-15 17:24:26,513] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:26,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:26,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:26,514] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:26,514] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:24:26,514] [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 17:24:26,514] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8078/tc_result.tsv
[2023-03-15 17:24:26,514] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:26,514] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:26,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference/checkm_data
[2023-03-15 17:24:26,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:26,520] [INFO] Task started: CheckM
[2023-03-15 17:24:26,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8078/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8078/checkm_input OceanDNA-b8078/checkm_result
[2023-03-15 17:24:48,140] [INFO] Task succeeded: CheckM
[2023-03-15 17:24:48,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:24:48,142] [INFO] ===== Completeness check finished =====
[2023-03-15 17:24:48,142] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:24:48,143] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8078/markers.fasta)
[2023-03-15 17:24:48,144] [INFO] Task started: Blastn
[2023-03-15 17:24:48,144] [INFO] Running command: blastn -query OceanDNA-b8078/markers.fasta -db /var/lib/cwl/stg95dc86be-8c85-4159-97d9-14485b9a2d2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8078/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:49,063] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:49,064] [INFO] Selected 10 target genomes.
[2023-03-15 17:24:49,064] [INFO] Target genome list was writen to OceanDNA-b8078/target_genomes_gtdb.txt
[2023-03-15 17:24:49,075] [INFO] Task started: fastANI
[2023-03-15 17:24:49,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgd305bd27-dc63-4379-b6d2-efba21f8a127/OceanDNA-b8078.fa --refList OceanDNA-b8078/target_genomes_gtdb.txt --output OceanDNA-b8078/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:24:51,838] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:51,843] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:24:51,843] [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_014239275.1	s__MAG-121220-bin8 sp014239275	94.1765	288	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	90.5717	243	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	86.4318	309	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	80.0239	203	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	79.4196	232	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	79.3303	207	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	77.3584	88	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_002705485.1	s__MAG-121220-bin8 sp002705485	76.5088	94	333	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.79	97.60	0.73	0.71	4	-
--------------------------------------------------------------------------------
[2023-03-15 17:24:51,844] [INFO] GTDB search result was written to OceanDNA-b8078/result_gtdb.tsv
[2023-03-15 17:24:51,844] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:24:51,844] [INFO] DFAST_QC result json was written to OceanDNA-b8078/dqc_result.json
[2023-03-15 17:24:51,845] [INFO] DFAST_QC completed!
[2023-03-15 17:24:51,845] [INFO] Total running time: 0h0m51s