[2023-03-15 12:44:24,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference
[2023-03-15 12:44:26,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,205] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,206] [INFO] Running command: cat /var/lib/cwl/stg1f1c8bbc-f536-4cc1-ac94-1f10243f173f/OceanDNA-b34860.fa | prodigal -d OceanDNA-b34860/cds.fna -a OceanDNA-b34860/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:36,780] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:36,781] [INFO] Task started: HMMsearch
[2023-03-15 12:44:36,781] [INFO] Running command: hmmsearch --tblout OceanDNA-b34860/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference/reference_markers.hmm OceanDNA-b34860/protein.faa > /dev/null
[2023-03-15 12:44:37,024] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:37,024] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1f1c8bbc-f536-4cc1-ac94-1f10243f173f/OceanDNA-b34860.fa]
[2023-03-15 12:44:37,042] [INFO] Query marker FASTA was written to OceanDNA-b34860/markers.fasta
[2023-03-15 12:44:37,043] [INFO] Task started: Blastn
[2023-03-15 12:44:37,043] [INFO] Running command: blastn -query OceanDNA-b34860/markers.fasta -db /var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference/reference_markers.fasta -out OceanDNA-b34860/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:37,688] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:37,689] [INFO] Selected 20 target genomes.
[2023-03-15 12:44:37,689] [INFO] Target genome list was writen to OceanDNA-b34860/target_genomes.txt
[2023-03-15 12:44:37,702] [INFO] Task started: fastANI
[2023-03-15 12:44:37,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f1c8bbc-f536-4cc1-ac94-1f10243f173f/OceanDNA-b34860.fa --refList OceanDNA-b34860/target_genomes.txt --output OceanDNA-b34860/fastani_result.tsv --threads 1
[2023-03-15 12:44:47,730] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:47,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:47,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:47,738] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:47,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:44:47,738] [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
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	80.7001	147	564	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	80.6318	146	564	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	79.7605	298	564	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	79.7189	123	564	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	79.5022	140	564	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	79.5009	139	564	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	79.4795	139	564	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	79.2655	185	564	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	78.1707	55	564	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	77.8477	55	564	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	77.8274	56	564	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:44:47,738] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34860/tc_result.tsv
[2023-03-15 12:44:47,739] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:47,739] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:47,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference/checkm_data
[2023-03-15 12:44:47,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:47,743] [INFO] Task started: CheckM
[2023-03-15 12:44:47,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34860/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34860/checkm_input OceanDNA-b34860/checkm_result
[2023-03-15 12:45:18,249] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:18,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:18,252] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:18,252] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:18,252] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34860/markers.fasta)
[2023-03-15 12:45:18,253] [INFO] Task started: Blastn
[2023-03-15 12:45:18,253] [INFO] Running command: blastn -query OceanDNA-b34860/markers.fasta -db /var/lib/cwl/stg79c7de9c-a14e-4967-b802-75f61d2a8b27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34860/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:19,237] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:19,238] [INFO] Selected 18 target genomes.
[2023-03-15 12:45:19,238] [INFO] Target genome list was writen to OceanDNA-b34860/target_genomes_gtdb.txt
[2023-03-15 12:45:19,279] [INFO] Task started: fastANI
[2023-03-15 12:45:19,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f1c8bbc-f536-4cc1-ac94-1f10243f173f/OceanDNA-b34860.fa --refList OceanDNA-b34860/target_genomes_gtdb.txt --output OceanDNA-b34860/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:28,371] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:28,377] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:45:28,378] [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_004362895.1	s__Idiomarina sp002729675	97.8887	544	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	conclusive
GCF_900100855.1	s__Idiomarina zobellii	80.6746	145	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987185.1	s__Idiomarina aquatica	79.765	297	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
GCF_000008465.1	s__Idiomarina loihiensis	79.7189	123	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_900116625.1	s__Idiomarina abyssalis	79.4999	138	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_003987095.1	s__Idiomarina piscisalsi	79.4885	139	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987275.1	s__Idiomarina seosinensis	79.2392	186	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987475.1	s__Idiomarina tyrosinivorans	78.1707	55	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	77.8696	54	564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:28,378] [INFO] GTDB search result was written to OceanDNA-b34860/result_gtdb.tsv
[2023-03-15 12:45:28,378] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:28,379] [INFO] DFAST_QC result json was written to OceanDNA-b34860/dqc_result.json
[2023-03-15 12:45:28,379] [INFO] DFAST_QC completed!
[2023-03-15 12:45:28,379] [INFO] Total running time: 0h1m4s