[2023-03-18 23:40:00,428] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,429] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,429] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference
[2023-03-18 23:40:01,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,529] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,529] [INFO] Running command: cat /var/lib/cwl/stg2948a957-1f71-499a-a088-adfa06920811/OceanDNA-b38613.fa | prodigal -d OceanDNA-b38613/cds.fna -a OceanDNA-b38613/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:17,369] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:17,370] [INFO] Task started: HMMsearch
[2023-03-18 23:40:17,370] [INFO] Running command: hmmsearch --tblout OceanDNA-b38613/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference/reference_markers.hmm OceanDNA-b38613/protein.faa > /dev/null
[2023-03-18 23:40:17,555] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:17,555] [INFO] Found 6/6 markers.
[2023-03-18 23:40:17,572] [INFO] Query marker FASTA was written to OceanDNA-b38613/markers.fasta
[2023-03-18 23:40:17,574] [INFO] Task started: Blastn
[2023-03-18 23:40:17,574] [INFO] Running command: blastn -query OceanDNA-b38613/markers.fasta -db /var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference/reference_markers.fasta -out OceanDNA-b38613/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:18,113] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:18,114] [INFO] Selected 13 target genomes.
[2023-03-18 23:40:18,115] [INFO] Target genome list was writen to OceanDNA-b38613/target_genomes.txt
[2023-03-18 23:40:18,121] [INFO] Task started: fastANI
[2023-03-18 23:40:18,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg2948a957-1f71-499a-a088-adfa06920811/OceanDNA-b38613.fa --refList OceanDNA-b38613/target_genomes.txt --output OceanDNA-b38613/fastani_result.tsv --threads 1
[2023-03-18 23:40:26,891] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:26,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:26,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:26,902] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:40:26,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:40:26,902] [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
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	97.9932	865	932	95	conclusive
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	82.2735	584	932	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	81.8496	663	932	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	81.2741	618	932	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	81.1855	612	932	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	81.1576	614	932	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	81.0551	540	932	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	81.0023	639	932	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.9625	617	932	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	80.927	624	932	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	80.14	521	932	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:40:26,903] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38613/tc_result.tsv
[2023-03-18 23:40:26,903] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:26,903] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:26,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference/checkm_data
[2023-03-18 23:40:26,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:26,908] [INFO] Task started: CheckM
[2023-03-18 23:40:26,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38613/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38613/checkm_input OceanDNA-b38613/checkm_result
[2023-03-18 23:41:09,011] [INFO] Task succeeded: CheckM
[2023-03-18 23:41:09,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:41:09,014] [INFO] ===== Completeness check finished =====
[2023-03-18 23:41:09,014] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:41:09,014] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38613/markers.fasta)
[2023-03-18 23:41:09,014] [INFO] Task started: Blastn
[2023-03-18 23:41:09,015] [INFO] Running command: blastn -query OceanDNA-b38613/markers.fasta -db /var/lib/cwl/stgdc612e6c-36d3-4edd-98a0-4c26ec59ad14/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38613/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:41:09,777] [INFO] Task succeeded: Blastn
[2023-03-18 23:41:09,778] [INFO] Selected 12 target genomes.
[2023-03-18 23:41:09,778] [INFO] Target genome list was writen to OceanDNA-b38613/target_genomes_gtdb.txt
[2023-03-18 23:41:09,791] [INFO] Task started: fastANI
[2023-03-18 23:41:09,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg2948a957-1f71-499a-a088-adfa06920811/OceanDNA-b38613.fa --refList OceanDNA-b38613/target_genomes_gtdb.txt --output OceanDNA-b38613/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:18,307] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:18,314] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 23:41:18,314] [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_900101915.1	s__Psychrobacter pacificensis	97.9868	865	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	inconclusive
GCF_001444505.1	s__Psychrobacter piscatorii	96.3171	800	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	97.27	96.69	0.93	0.91	3	inconclusive
GCF_904846415.1	s__Psychrobacter piscatorii_A	92.3283	808	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836735.1	s__Psychrobacter sp002836735	84.7194	759	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_002836715.1	s__Psychrobacter sp002836715	84.6772	723	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812035.1	s__Psychrobacter nivimaris_A	84.6657	737	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000586435.1	s__Psychrobacter sp000586435	84.2253	733	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350005.1	s__Psychrobacter proteolyticus_A	84.2246	756	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.98	99.95	0.99	0.99	4	-
GCF_014770435.1	s__Psychrobacter sp014770435	84.1003	733	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435845.1	s__Psychrobacter sp001435845	84.0882	749	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163785.1	s__Psychrobacter alimentarius	81.7775	617	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.11	97.08	0.93	0.93	3	-
GCA_001411745.2	s__Psychrobacter glacincola_A	80.9451	607	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:18,315] [INFO] GTDB search result was written to OceanDNA-b38613/result_gtdb.tsv
[2023-03-18 23:41:18,315] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:18,317] [INFO] DFAST_QC result json was written to OceanDNA-b38613/dqc_result.json
[2023-03-18 23:41:18,317] [INFO] DFAST_QC completed!
[2023-03-18 23:41:18,317] [INFO] Total running time: 0h1m18s