[2023-03-15 10:34:47,907] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference
[2023-03-15 10:34:49,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stgd486081a-1bb0-420a-98f3-682a4ec6be14/OceanDNA-b10095.fa | prodigal -d OceanDNA-b10095/cds.fna -a OceanDNA-b10095/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:34:59,135] [INFO] Task succeeded: Prodigal
[2023-03-15 10:34:59,136] [INFO] Task started: HMMsearch
[2023-03-15 10:34:59,136] [INFO] Running command: hmmsearch --tblout OceanDNA-b10095/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference/reference_markers.hmm OceanDNA-b10095/protein.faa > /dev/null
[2023-03-15 10:34:59,318] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:34:59,319] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd486081a-1bb0-420a-98f3-682a4ec6be14/OceanDNA-b10095.fa]
[2023-03-15 10:34:59,437] [INFO] Query marker FASTA was written to OceanDNA-b10095/markers.fasta
[2023-03-15 10:34:59,437] [INFO] Task started: Blastn
[2023-03-15 10:34:59,437] [INFO] Running command: blastn -query OceanDNA-b10095/markers.fasta -db /var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference/reference_markers.fasta -out OceanDNA-b10095/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:34:59,985] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:00,029] [INFO] Selected 22 target genomes.
[2023-03-15 10:35:00,029] [INFO] Target genome list was writen to OceanDNA-b10095/target_genomes.txt
[2023-03-15 10:35:00,039] [INFO] Task started: fastANI
[2023-03-15 10:35:00,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgd486081a-1bb0-420a-98f3-682a4ec6be14/OceanDNA-b10095.fa --refList OceanDNA-b10095/target_genomes.txt --output OceanDNA-b10095/fastani_result.tsv --threads 1
[2023-03-15 10:35:12,366] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:12,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:12,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:12,370] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:12,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:35:12,370] [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
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.0757	67	246	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.0539	73	246	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:35:12,388] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10095/tc_result.tsv
[2023-03-15 10:35:12,414] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:12,414] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:12,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference/checkm_data
[2023-03-15 10:35:12,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:12,450] [INFO] Task started: CheckM
[2023-03-15 10:35:12,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10095/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10095/checkm_input OceanDNA-b10095/checkm_result
[2023-03-15 10:35:42,996] [INFO] Task succeeded: CheckM
[2023-03-15 10:35:42,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.16%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:35:43,254] [INFO] ===== Completeness check finished =====
[2023-03-15 10:35:43,254] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:35:43,254] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10095/markers.fasta)
[2023-03-15 10:35:43,255] [INFO] Task started: Blastn
[2023-03-15 10:35:43,255] [INFO] Running command: blastn -query OceanDNA-b10095/markers.fasta -db /var/lib/cwl/stg3068d621-c4c1-4d71-8bb5-bc6786ee7fe7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10095/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:43,988] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:44,034] [INFO] Selected 19 target genomes.
[2023-03-15 10:35:44,034] [INFO] Target genome list was writen to OceanDNA-b10095/target_genomes_gtdb.txt
[2023-03-15 10:35:44,505] [INFO] Task started: fastANI
[2023-03-15 10:35:44,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgd486081a-1bb0-420a-98f3-682a4ec6be14/OceanDNA-b10095.fa --refList OceanDNA-b10095/target_genomes_gtdb.txt --output OceanDNA-b10095/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:35:54,988] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:54,993] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:35:54,993] [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_017643165.1	s__Psychroserpens sp017643165	77.3896	56	246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.99	99.97	1.00	1.00	7	-
GCF_000826645.1	s__Psychroserpens mesophilus	77.3477	71	246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	77.2572	80	246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.0539	73	246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	77.0037	59	246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.4363	51	246	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:35:55,011] [INFO] GTDB search result was written to OceanDNA-b10095/result_gtdb.tsv
[2023-03-15 10:35:55,037] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:35:55,054] [INFO] DFAST_QC result json was written to OceanDNA-b10095/dqc_result.json
[2023-03-15 10:35:55,054] [INFO] DFAST_QC completed!
[2023-03-15 10:35:55,054] [INFO] Total running time: 0h1m7s