[2023-03-16 10:41:52,508] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:41:52,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:41:52,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference
[2023-03-16 10:41:54,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:41:54,838] [INFO] Task started: Prodigal
[2023-03-16 10:41:54,838] [INFO] Running command: cat /var/lib/cwl/stgc0170778-a7c6-4309-8e4a-9e86425a38c7/OceanDNA-b34805.fa | prodigal -d OceanDNA-b34805/cds.fna -a OceanDNA-b34805/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:42:15,351] [INFO] Task succeeded: Prodigal
[2023-03-16 10:42:15,352] [INFO] Task started: HMMsearch
[2023-03-16 10:42:15,352] [INFO] Running command: hmmsearch --tblout OceanDNA-b34805/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference/reference_markers.hmm OceanDNA-b34805/protein.faa > /dev/null
[2023-03-16 10:42:15,555] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:42:15,555] [INFO] Found 6/6 markers.
[2023-03-16 10:42:15,569] [INFO] Query marker FASTA was written to OceanDNA-b34805/markers.fasta
[2023-03-16 10:42:15,571] [INFO] Task started: Blastn
[2023-03-16 10:42:15,571] [INFO] Running command: blastn -query OceanDNA-b34805/markers.fasta -db /var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference/reference_markers.fasta -out OceanDNA-b34805/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:42:16,316] [INFO] Task succeeded: Blastn
[2023-03-16 10:42:16,317] [INFO] Selected 19 target genomes.
[2023-03-16 10:42:16,317] [INFO] Target genome list was writen to OceanDNA-b34805/target_genomes.txt
[2023-03-16 10:42:16,329] [INFO] Task started: fastANI
[2023-03-16 10:42:16,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0170778-a7c6-4309-8e4a-9e86425a38c7/OceanDNA-b34805.fa --refList OceanDNA-b34805/target_genomes.txt --output OceanDNA-b34805/fastani_result.tsv --threads 1
[2023-03-16 10:42:26,833] [INFO] Task succeeded: fastANI
[2023-03-16 10:42:26,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:42:26,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:42:26,891] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 10:42:26,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 10:42:26,891] [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 gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	98.0035	691	710	95	conclusive
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	80.4655	393	710	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	80.2759	394	710	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	80.1054	366	710	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	80.1054	366	710	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	80.0809	404	710	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	79.8814	375	710	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	79.8688	375	710	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_000753715.1	435908	435908	type	True	78.2647	139	710	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_003987105.1	435908	435908	type	True	78.2642	137	710	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:42:26,891] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34805/tc_result.tsv
[2023-03-16 10:42:26,891] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:42:26,892] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:42:26,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference/checkm_data
[2023-03-16 10:42:26,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:42:27,241] [INFO] Task started: CheckM
[2023-03-16 10:42:27,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34805/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34805/checkm_input OceanDNA-b34805/checkm_result
[2023-03-16 10:43:13,564] [INFO] Task succeeded: CheckM
[2023-03-16 10:43:13,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:43:13,567] [INFO] ===== Completeness check finished =====
[2023-03-16 10:43:13,567] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:43:13,567] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34805/markers.fasta)
[2023-03-16 10:43:13,568] [INFO] Task started: Blastn
[2023-03-16 10:43:13,568] [INFO] Running command: blastn -query OceanDNA-b34805/markers.fasta -db /var/lib/cwl/stg3bdcfe93-da41-4c86-9717-22c8ca936273/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34805/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:43:14,813] [INFO] Task succeeded: Blastn
[2023-03-16 10:43:14,814] [INFO] Selected 16 target genomes.
[2023-03-16 10:43:14,814] [INFO] Target genome list was writen to OceanDNA-b34805/target_genomes_gtdb.txt
[2023-03-16 10:43:14,833] [INFO] Task started: fastANI
[2023-03-16 10:43:14,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0170778-a7c6-4309-8e4a-9e86425a38c7/OceanDNA-b34805.fa --refList OceanDNA-b34805/target_genomes_gtdb.txt --output OceanDNA-b34805/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:43:22,061] [INFO] Task succeeded: fastANI
[2023-03-16 10:43:22,071] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:43:22,071] [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_004025325.1	s__Pseudidiomarina gelatinasegens	98.0035	691	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002279005.1	s__Pseudidiomarina sp002279005	80.7052	321	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	80.5707	402	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987045.1	s__Pseudidiomarina marina	80.4655	393	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_001418345.1	s__Pseudidiomarina woesei	80.1054	366	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	80.0673	405	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	79.9054	374	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	79.8688	375	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	79.1665	201	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	78.9132	154	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003987225.1	s__Pseudidiomarina homiensis	78.4188	153	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.2647	139	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002423905.1	s__Pseudidiomarina sp002423905	77.6202	107	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:43:22,071] [INFO] GTDB search result was written to OceanDNA-b34805/result_gtdb.tsv
[2023-03-16 10:43:22,071] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:43:22,073] [INFO] DFAST_QC result json was written to OceanDNA-b34805/dqc_result.json
[2023-03-16 10:43:22,073] [INFO] DFAST_QC completed!
[2023-03-16 10:43:22,073] [INFO] Total running time: 0h1m30s