[2023-03-18 08:17:17,728] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference
[2023-03-18 08:17:18,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg60a10282-1260-4bce-8b81-94e75e7094f4/OceanDNA-b34944.fa | prodigal -d OceanDNA-b34944/cds.fna -a OceanDNA-b34944/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:35,306] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:35,306] [INFO] Task started: HMMsearch
[2023-03-18 08:17:35,306] [INFO] Running command: hmmsearch --tblout OceanDNA-b34944/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference/reference_markers.hmm OceanDNA-b34944/protein.faa > /dev/null
[2023-03-18 08:17:35,645] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:35,646] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg60a10282-1260-4bce-8b81-94e75e7094f4/OceanDNA-b34944.fa]
[2023-03-18 08:17:35,681] [INFO] Query marker FASTA was written to OceanDNA-b34944/markers.fasta
[2023-03-18 08:17:35,682] [INFO] Task started: Blastn
[2023-03-18 08:17:35,682] [INFO] Running command: blastn -query OceanDNA-b34944/markers.fasta -db /var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference/reference_markers.fasta -out OceanDNA-b34944/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:36,237] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:36,238] [INFO] Selected 14 target genomes.
[2023-03-18 08:17:36,238] [INFO] Target genome list was writen to OceanDNA-b34944/target_genomes.txt
[2023-03-18 08:17:36,247] [INFO] Task started: fastANI
[2023-03-18 08:17:36,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg60a10282-1260-4bce-8b81-94e75e7094f4/OceanDNA-b34944.fa --refList OceanDNA-b34944/target_genomes.txt --output OceanDNA-b34944/fastani_result.tsv --threads 1
[2023-03-18 08:17:48,576] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:48,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:48,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:48,584] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:48,584] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:48,584] [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
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	90.2715	887	1011	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	90.2523	886	1011	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	90.2008	819	1011	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	77.5823	181	1011	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	77.5551	153	1011	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	77.5293	152	1011	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.3238	178	1011	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	77.2923	164	1011	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.1289	138	1011	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	77.097	116	1011	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.5641	126	1011	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:48,584] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34944/tc_result.tsv
[2023-03-18 08:17:48,584] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:48,584] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:48,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference/checkm_data
[2023-03-18 08:17:48,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:48,590] [INFO] Task started: CheckM
[2023-03-18 08:17:48,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34944/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34944/checkm_input OceanDNA-b34944/checkm_result
[2023-03-18 08:18:31,845] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:31,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:31,849] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:31,849] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:31,849] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34944/markers.fasta)
[2023-03-18 08:18:31,849] [INFO] Task started: Blastn
[2023-03-18 08:18:31,849] [INFO] Running command: blastn -query OceanDNA-b34944/markers.fasta -db /var/lib/cwl/stg99aed57b-d688-4dd7-889a-dc69397a9c1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34944/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:32,641] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:32,641] [INFO] Selected 14 target genomes.
[2023-03-18 08:18:32,641] [INFO] Target genome list was writen to OceanDNA-b34944/target_genomes_gtdb.txt
[2023-03-18 08:18:32,653] [INFO] Task started: fastANI
[2023-03-18 08:18:32,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg60a10282-1260-4bce-8b81-94e75e7094f4/OceanDNA-b34944.fa --refList OceanDNA-b34944/target_genomes_gtdb.txt --output OceanDNA-b34944/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:43,182] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:43,190] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:43,209] [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_005876835.1	s__Pseudoalteromonas phenolica_B	93.8512	906	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	90.2523	886	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_005886345.1	s__Pseudoalteromonas phenolica_A	90.1733	781	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	77.6731	183	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238375.3	s__Pseudoalteromonas citrea	77.5823	181	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176705.1	s__Pseudoalteromonas sp009176705	77.5684	174	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	77.5626	150	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814765.1	s__Pseudoalteromonas luteoviolacea_H	77.4678	148	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.92	0.92	2	-
GCF_004103285.1	s__Pseudoalteromonas sp004103285	77.4308	154	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.27	99.27	0.97	0.97	2	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.3075	179	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	77.2973	163	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	77.2923	164	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.2139	178	1011	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:43,209] [INFO] GTDB search result was written to OceanDNA-b34944/result_gtdb.tsv
[2023-03-18 08:18:43,209] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:43,210] [INFO] DFAST_QC result json was written to OceanDNA-b34944/dqc_result.json
[2023-03-18 08:18:43,211] [INFO] DFAST_QC completed!
[2023-03-18 08:18:43,211] [INFO] Total running time: 0h1m25s