[2023-03-15 11:51:17,347] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference
[2023-03-15 11:51:18,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,955] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,955] [INFO] Running command: cat /var/lib/cwl/stge4e63bd8-c8f5-45ad-9d36-c603eef6745b/OceanDNA-b10602.fa | prodigal -d OceanDNA-b10602/cds.fna -a OceanDNA-b10602/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:28,422] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:28,422] [INFO] Task started: HMMsearch
[2023-03-15 11:51:28,422] [INFO] Running command: hmmsearch --tblout OceanDNA-b10602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference/reference_markers.hmm OceanDNA-b10602/protein.faa > /dev/null
[2023-03-15 11:51:28,606] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:28,607] [INFO] Found 6/6 markers.
[2023-03-15 11:51:28,619] [INFO] Query marker FASTA was written to OceanDNA-b10602/markers.fasta
[2023-03-15 11:51:28,619] [INFO] Task started: Blastn
[2023-03-15 11:51:28,619] [INFO] Running command: blastn -query OceanDNA-b10602/markers.fasta -db /var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference/reference_markers.fasta -out OceanDNA-b10602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:29,201] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:29,202] [INFO] Selected 31 target genomes.
[2023-03-15 11:51:29,202] [INFO] Target genome list was writen to OceanDNA-b10602/target_genomes.txt
[2023-03-15 11:51:29,223] [INFO] Task started: fastANI
[2023-03-15 11:51:29,223] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e63bd8-c8f5-45ad-9d36-c603eef6745b/OceanDNA-b10602.fa --refList OceanDNA-b10602/target_genomes.txt --output OceanDNA-b10602/fastani_result.tsv --threads 1
[2023-03-15 11:51:46,637] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:46,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:46,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:46,643] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:46,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:46,643] [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
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.1353	51	430	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.1057	51	430	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.0167	52	430	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	75.9497	50	430	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:46,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10602/tc_result.tsv
[2023-03-15 11:51:46,643] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:46,643] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:46,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference/checkm_data
[2023-03-15 11:51:46,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:46,647] [INFO] Task started: CheckM
[2023-03-15 11:51:46,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10602/checkm_input OceanDNA-b10602/checkm_result
[2023-03-15 11:52:15,767] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:15,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:15,769] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:15,769] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:15,769] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10602/markers.fasta)
[2023-03-15 11:52:15,770] [INFO] Task started: Blastn
[2023-03-15 11:52:15,770] [INFO] Running command: blastn -query OceanDNA-b10602/markers.fasta -db /var/lib/cwl/stg55032d9b-73a7-44b4-a7dc-faeac3459c22/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:16,601] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:16,602] [INFO] Selected 28 target genomes.
[2023-03-15 11:52:16,602] [INFO] Target genome list was writen to OceanDNA-b10602/target_genomes_gtdb.txt
[2023-03-15 11:52:16,631] [INFO] Task started: fastANI
[2023-03-15 11:52:16,631] [INFO] Running command: fastANI --query /var/lib/cwl/stge4e63bd8-c8f5-45ad-9d36-c603eef6745b/OceanDNA-b10602.fa --refList OceanDNA-b10602/target_genomes_gtdb.txt --output OceanDNA-b10602/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:28,416] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:28,425] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:52:28,426] [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_001735715.1	s__GCA001735715 sp001735715	97.3139	415	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	conclusive
GCA_018673215.1	s__Hel1-33-131 sp018673215	81.7517	105	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690085.1	s__UBA3537 sp002690085	77.2609	81	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709185.1	s__UBA3537 sp002709185	77.0819	68	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_002684355.1	s__UBA3537 sp002684355	76.983	102	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.7516	83	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725015.1	s__UBA3537 sp002725015	76.6083	69	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	76.4606	62	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	76.3826	64	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	76.3597	76	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698705.1	s__UBA3537 sp002698705	76.3392	82	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	76.2257	79	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	75.9604	85	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	75.9497	50	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	75.8239	53	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:28,426] [INFO] GTDB search result was written to OceanDNA-b10602/result_gtdb.tsv
[2023-03-15 11:52:28,426] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:28,427] [INFO] DFAST_QC result json was written to OceanDNA-b10602/dqc_result.json
[2023-03-15 11:52:28,427] [INFO] DFAST_QC completed!
[2023-03-15 11:52:28,427] [INFO] Total running time: 0h1m11s