[2023-03-16 01:12:29,291] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,295] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,295] [INFO] DQC Reference Directory: /var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference
[2023-03-16 01:12:30,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,461] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stga34a0277-d18e-413b-b6b8-c3ea2e2f4d89/OceanDNA-b34850.fa | prodigal -d OceanDNA-b34850/cds.fna -a OceanDNA-b34850/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:46,936] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:46,936] [INFO] Task started: HMMsearch
[2023-03-16 01:12:46,936] [INFO] Running command: hmmsearch --tblout OceanDNA-b34850/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference/reference_markers.hmm OceanDNA-b34850/protein.faa > /dev/null
[2023-03-16 01:12:47,143] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:47,144] [INFO] Found 6/6 markers.
[2023-03-16 01:12:47,169] [INFO] Query marker FASTA was written to OceanDNA-b34850/markers.fasta
[2023-03-16 01:12:47,170] [INFO] Task started: Blastn
[2023-03-16 01:12:47,170] [INFO] Running command: blastn -query OceanDNA-b34850/markers.fasta -db /var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference/reference_markers.fasta -out OceanDNA-b34850/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:47,822] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:47,824] [INFO] Selected 17 target genomes.
[2023-03-16 01:12:47,825] [INFO] Target genome list was writen to OceanDNA-b34850/target_genomes.txt
[2023-03-16 01:12:47,905] [INFO] Task started: fastANI
[2023-03-16 01:12:47,905] [INFO] Running command: fastANI --query /var/lib/cwl/stga34a0277-d18e-413b-b6b8-c3ea2e2f4d89/OceanDNA-b34850.fa --refList OceanDNA-b34850/target_genomes.txt --output OceanDNA-b34850/fastani_result.tsv --threads 1
[2023-03-16 01:12:57,688] [INFO] Task succeeded: fastANI
[2023-03-16 01:12:57,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:12:57,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:12:57,694] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 01:12:57,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 01:12:57,694] [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 loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	96.8615	837	967	95	conclusive
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	84.8035	655	967	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	84.6652	648	967	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	84.6541	657	967	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	80.7701	406	967	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	80.7141	408	967	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	79.9004	395	967	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	77.5127	118	967	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:12:57,699] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34850/tc_result.tsv
[2023-03-16 01:12:57,709] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:12:57,709] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:12:57,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference/checkm_data
[2023-03-16 01:12:57,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:12:57,726] [INFO] Task started: CheckM
[2023-03-16 01:12:57,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34850/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34850/checkm_input OceanDNA-b34850/checkm_result
[2023-03-16 01:13:40,989] [INFO] Task succeeded: CheckM
[2023-03-16 01:13:40,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:13:40,998] [INFO] ===== Completeness check finished =====
[2023-03-16 01:13:40,998] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:13:40,998] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34850/markers.fasta)
[2023-03-16 01:13:40,999] [INFO] Task started: Blastn
[2023-03-16 01:13:40,999] [INFO] Running command: blastn -query OceanDNA-b34850/markers.fasta -db /var/lib/cwl/stgec704553-f926-4797-b482-403f636638ac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34850/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:42,057] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:42,061] [INFO] Selected 13 target genomes.
[2023-03-16 01:13:42,061] [INFO] Target genome list was writen to OceanDNA-b34850/target_genomes_gtdb.txt
[2023-03-16 01:13:42,593] [INFO] Task started: fastANI
[2023-03-16 01:13:42,593] [INFO] Running command: fastANI --query /var/lib/cwl/stga34a0277-d18e-413b-b6b8-c3ea2e2f4d89/OceanDNA-b34850.fa --refList OceanDNA-b34850/target_genomes_gtdb.txt --output OceanDNA-b34850/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:13:50,407] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:50,413] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:13:50,413] [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_000008465.1	s__Idiomarina loihiensis	96.8347	838	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	conclusive
GCF_003987255.1	s__Idiomarina ramblicola	84.8035	655	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	84.6541	657	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_900100855.1	s__Idiomarina zobellii	80.7129	407	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987095.1	s__Idiomarina piscisalsi	79.901	396	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	79.7649	387	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003987185.1	s__Idiomarina aquatica	78.8501	223	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	77.5211	102	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.5127	118	967	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 01:13:50,415] [INFO] GTDB search result was written to OceanDNA-b34850/result_gtdb.tsv
[2023-03-16 01:13:50,416] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:13:50,419] [INFO] DFAST_QC result json was written to OceanDNA-b34850/dqc_result.json
[2023-03-16 01:13:50,419] [INFO] DFAST_QC completed!
[2023-03-16 01:13:50,419] [INFO] Total running time: 0h1m21s