[2023-03-15 15:55:16,219] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,219] [INFO] DQC Reference Directory: /var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,912] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,912] [INFO] Running command: cat /var/lib/cwl/stg525601f2-a15c-426c-8b3e-e63b44353ce2/OceanDNA-b34859.fa | prodigal -d OceanDNA-b34859/cds.fna -a OceanDNA-b34859/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:29,996] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:29,997] [INFO] Task started: HMMsearch
[2023-03-15 15:55:29,997] [INFO] Running command: hmmsearch --tblout OceanDNA-b34859/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference/reference_markers.hmm OceanDNA-b34859/protein.faa > /dev/null
[2023-03-15 15:55:30,181] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:30,182] [INFO] Found 6/6 markers.
[2023-03-15 15:55:30,199] [INFO] Query marker FASTA was written to OceanDNA-b34859/markers.fasta
[2023-03-15 15:55:30,202] [INFO] Task started: Blastn
[2023-03-15 15:55:30,202] [INFO] Running command: blastn -query OceanDNA-b34859/markers.fasta -db /var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference/reference_markers.fasta -out OceanDNA-b34859/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:30,844] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:30,845] [INFO] Selected 21 target genomes.
[2023-03-15 15:55:30,846] [INFO] Target genome list was writen to OceanDNA-b34859/target_genomes.txt
[2023-03-15 15:55:30,859] [INFO] Task started: fastANI
[2023-03-15 15:55:30,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg525601f2-a15c-426c-8b3e-e63b44353ce2/OceanDNA-b34859.fa --refList OceanDNA-b34859/target_genomes.txt --output OceanDNA-b34859/fastani_result.tsv --threads 1
[2023-03-15 15:55:42,783] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:42,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:42,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:42,792] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 15:55:42,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 15:55:42,792] [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
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	97.2736	624	665	95	conclusive
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	82.594	434	665	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	79.7739	287	665	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	79.2931	253	665	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	79.25	248	665	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	79.1416	242	665	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	78.8119	263	665	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	78.7668	161	665	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	78.3986	152	665	95	below_threshold
Pseudidiomarina taiwanensis	strain=PIT1	GCA_003987435.1	337250	337250	type	True	78.1412	108	665	95	below_threshold
Idiomarina mangrovi	strain=ZQ330	GCA_003999375.1	2487133	2487133	type	True	77.7999	117	665	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	77.7521	71	665	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:42,792] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34859/tc_result.tsv
[2023-03-15 15:55:42,792] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:42,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:42,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference/checkm_data
[2023-03-15 15:55:42,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:42,797] [INFO] Task started: CheckM
[2023-03-15 15:55:42,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34859/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34859/checkm_input OceanDNA-b34859/checkm_result
[2023-03-15 15:56:17,061] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:17,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:17,064] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:17,064] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:17,065] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34859/markers.fasta)
[2023-03-15 15:56:17,065] [INFO] Task started: Blastn
[2023-03-15 15:56:17,065] [INFO] Running command: blastn -query OceanDNA-b34859/markers.fasta -db /var/lib/cwl/stgc68955a0-c473-4436-90fd-06c294df3aaa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34859/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:18,004] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:18,005] [INFO] Selected 18 target genomes.
[2023-03-15 15:56:18,006] [INFO] Target genome list was writen to OceanDNA-b34859/target_genomes_gtdb.txt
[2023-03-15 15:56:18,016] [INFO] Task started: fastANI
[2023-03-15 15:56:18,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg525601f2-a15c-426c-8b3e-e63b44353ce2/OceanDNA-b34859.fa --refList OceanDNA-b34859/target_genomes_gtdb.txt --output OceanDNA-b34859/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:27,227] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:27,235] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:56:27,235] [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_003987395.1	s__Pseudidiomarina aquimaris	97.2736	624	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	conclusive
GCF_003987225.1	s__Pseudidiomarina homiensis	82.613	433	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	79.7556	288	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	79.2931	253	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902806985.1	s__Pseudidiomarina piscicola	79.1416	242	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	79.0099	142	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	78.9584	162	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_003987215.1	s__Pseudidiomarina halophila	78.8119	263	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418345.1	s__Pseudidiomarina woesei	78.7668	161	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	78.6449	156	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987435.1	s__Pseudidiomarina taiwanensis	78.1412	108	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	77.7999	117	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987185.1	s__Idiomarina aquatica	77.7521	71	665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:27,247] [INFO] GTDB search result was written to OceanDNA-b34859/result_gtdb.tsv
[2023-03-15 15:56:27,247] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:27,248] [INFO] DFAST_QC result json was written to OceanDNA-b34859/dqc_result.json
[2023-03-15 15:56:27,249] [INFO] DFAST_QC completed!
[2023-03-15 15:56:27,249] [INFO] Total running time: 0h1m11s