[2023-03-19 02:44:00,524] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:44:00,524] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:44:00,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference
[2023-03-19 02:44:06,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:44:06,100] [INFO] Task started: Prodigal
[2023-03-19 02:44:06,100] [INFO] Running command: cat /var/lib/cwl/stg4fb4fb8f-294c-4d3e-a88c-c3892d72e112/OceanDNA-b10093.fa | prodigal -d OceanDNA-b10093/cds.fna -a OceanDNA-b10093/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:44:24,985] [INFO] Task succeeded: Prodigal
[2023-03-19 02:44:24,985] [INFO] Task started: HMMsearch
[2023-03-19 02:44:24,985] [INFO] Running command: hmmsearch --tblout OceanDNA-b10093/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference/reference_markers.hmm OceanDNA-b10093/protein.faa > /dev/null
[2023-03-19 02:44:25,186] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:44:25,187] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4fb4fb8f-294c-4d3e-a88c-c3892d72e112/OceanDNA-b10093.fa]
[2023-03-19 02:44:25,205] [INFO] Query marker FASTA was written to OceanDNA-b10093/markers.fasta
[2023-03-19 02:44:25,207] [INFO] Task started: Blastn
[2023-03-19 02:44:25,207] [INFO] Running command: blastn -query OceanDNA-b10093/markers.fasta -db /var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference/reference_markers.fasta -out OceanDNA-b10093/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:44:28,896] [INFO] Task succeeded: Blastn
[2023-03-19 02:44:28,897] [INFO] Selected 25 target genomes.
[2023-03-19 02:44:28,897] [INFO] Target genome list was writen to OceanDNA-b10093/target_genomes.txt
[2023-03-19 02:44:28,969] [INFO] Task started: fastANI
[2023-03-19 02:44:28,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb4fb8f-294c-4d3e-a88c-c3892d72e112/OceanDNA-b10093.fa --refList OceanDNA-b10093/target_genomes.txt --output OceanDNA-b10093/fastani_result.tsv --threads 1
[2023-03-19 02:44:44,343] [INFO] Task succeeded: fastANI
[2023-03-19 02:44:44,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:44:44,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:44:44,400] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:44:44,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:44:44,401] [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	78.0847	339	1004	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.8787	309	1004	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.5625	277	1004	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.276	205	1004	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	77.1185	219	1004	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.9621	218	1004	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.924	209	1004	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.8938	211	1004	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.8188	163	1004	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.773	168	1004	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.7663	225	1004	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	76.75	148	1004	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.7074	150	1004	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.6986	211	1004	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.6608	219	1004	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.5295	140	1004	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.4575	135	1004	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.4345	134	1004	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.3018	132	1004	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.2137	128	1004	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.1181	120	1004	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.0952	121	1004	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.0851	103	1004	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	75.6668	67	1004	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:44:44,401] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10093/tc_result.tsv
[2023-03-19 02:44:44,401] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:44:44,401] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:44:44,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference/checkm_data
[2023-03-19 02:44:44,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:44:44,407] [INFO] Task started: CheckM
[2023-03-19 02:44:44,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10093/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10093/checkm_input OceanDNA-b10093/checkm_result
[2023-03-19 02:45:38,345] [INFO] Task succeeded: CheckM
[2023-03-19 02:45:38,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:45:38,349] [INFO] ===== Completeness check finished =====
[2023-03-19 02:45:38,349] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:45:38,350] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10093/markers.fasta)
[2023-03-19 02:45:38,351] [INFO] Task started: Blastn
[2023-03-19 02:45:38,351] [INFO] Running command: blastn -query OceanDNA-b10093/markers.fasta -db /var/lib/cwl/stg8300c6be-45da-480c-971e-09d40c79d269/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10093/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:45:39,489] [INFO] Task succeeded: Blastn
[2023-03-19 02:45:39,491] [INFO] Selected 8 target genomes.
[2023-03-19 02:45:39,491] [INFO] Target genome list was writen to OceanDNA-b10093/target_genomes_gtdb.txt
[2023-03-19 02:45:39,567] [INFO] Task started: fastANI
[2023-03-19 02:45:39,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb4fb8f-294c-4d3e-a88c-c3892d72e112/OceanDNA-b10093.fa --refList OceanDNA-b10093/target_genomes_gtdb.txt --output OceanDNA-b10093/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:45:45,545] [INFO] Task succeeded: fastANI
[2023-03-19 02:45:45,551] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:45:45,551] [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_000425305.1	s__Psychroserpens burtonensis	84.3993	719	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCA_905479815.1	s__Psychroserpens sp905479815	81.4981	526	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	81.229	643	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	79.8509	527	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	78.6312	455	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	78.2235	389	1004	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	77.8787	309	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.2872	133	1004	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:45:45,553] [INFO] GTDB search result was written to OceanDNA-b10093/result_gtdb.tsv
[2023-03-19 02:45:45,556] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:45:45,560] [INFO] DFAST_QC result json was written to OceanDNA-b10093/dqc_result.json
[2023-03-19 02:45:45,560] [INFO] DFAST_QC completed!
[2023-03-19 02:45:45,560] [INFO] Total running time: 0h1m45s