[2023-03-14 12:44:46,931] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:44:46,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:44:46,931] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference
[2023-03-14 12:44:48,028] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:44:48,028] [INFO] Task started: Prodigal
[2023-03-14 12:44:48,028] [INFO] Running command: cat /var/lib/cwl/stg65b4cb45-ffce-42b4-992e-cd5090e349cd/OceanDNA-b34950.fa | prodigal -d OceanDNA-b34950/cds.fna -a OceanDNA-b34950/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:45:02,979] [INFO] Task succeeded: Prodigal
[2023-03-14 12:45:02,979] [INFO] Task started: HMMsearch
[2023-03-14 12:45:02,979] [INFO] Running command: hmmsearch --tblout OceanDNA-b34950/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference/reference_markers.hmm OceanDNA-b34950/protein.faa > /dev/null
[2023-03-14 12:45:03,201] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:45:03,202] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg65b4cb45-ffce-42b4-992e-cd5090e349cd/OceanDNA-b34950.fa]
[2023-03-14 12:45:03,241] [INFO] Query marker FASTA was written to OceanDNA-b34950/markers.fasta
[2023-03-14 12:45:03,245] [INFO] Task started: Blastn
[2023-03-14 12:45:03,245] [INFO] Running command: blastn -query OceanDNA-b34950/markers.fasta -db /var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference/reference_markers.fasta -out OceanDNA-b34950/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:45:03,820] [INFO] Task succeeded: Blastn
[2023-03-14 12:45:03,822] [INFO] Selected 18 target genomes.
[2023-03-14 12:45:03,822] [INFO] Target genome list was writen to OceanDNA-b34950/target_genomes.txt
[2023-03-14 12:45:03,835] [INFO] Task started: fastANI
[2023-03-14 12:45:03,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b4cb45-ffce-42b4-992e-cd5090e349cd/OceanDNA-b34950.fa --refList OceanDNA-b34950/target_genomes.txt --output OceanDNA-b34950/fastani_result.tsv --threads 1
[2023-03-14 12:45:18,653] [INFO] Task succeeded: fastANI
[2023-03-14 12:45:18,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:45:18,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:45:18,663] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:45:18,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:45:18,664] [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 prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	81.4127	530	891	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	81.3907	526	891	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	81.0677	492	891	95	below_threshold
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	80.9712	484	891	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.8104	533	891	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	79.9648	379	891	95	below_threshold
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	79.9093	367	891	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	79.8513	357	891	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	79.7371	390	891	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	79.6901	379	891	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	79.6859	400	891	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	79.5122	397	891	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	79.4013	378	891	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	79.3753	384	891	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:45:18,664] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34950/tc_result.tsv
[2023-03-14 12:45:18,664] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:45:18,665] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:45:18,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference/checkm_data
[2023-03-14 12:45:18,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:45:18,671] [INFO] Task started: CheckM
[2023-03-14 12:45:18,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34950/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34950/checkm_input OceanDNA-b34950/checkm_result
[2023-03-14 12:46:09,155] [INFO] Task succeeded: CheckM
[2023-03-14 12:46:09,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:46:09,317] [INFO] ===== Completeness check finished =====
[2023-03-14 12:46:09,317] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:46:09,317] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34950/markers.fasta)
[2023-03-14 12:46:09,318] [INFO] Task started: Blastn
[2023-03-14 12:46:09,318] [INFO] Running command: blastn -query OceanDNA-b34950/markers.fasta -db /var/lib/cwl/stgcd079632-c51c-445d-8592-daa472ea0e7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34950/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:46:10,180] [INFO] Task succeeded: Blastn
[2023-03-14 12:46:10,181] [INFO] Selected 12 target genomes.
[2023-03-14 12:46:10,181] [INFO] Target genome list was writen to OceanDNA-b34950/target_genomes_gtdb.txt
[2023-03-14 12:46:10,196] [INFO] Task started: fastANI
[2023-03-14 12:46:10,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg65b4cb45-ffce-42b4-992e-cd5090e349cd/OceanDNA-b34950.fa --refList OceanDNA-b34950/target_genomes_gtdb.txt --output OceanDNA-b34950/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:46:22,927] [INFO] Task succeeded: fastANI
[2023-03-14 12:46:22,936] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:46:22,936] [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_002723455.1	s__Pseudoalteromonas sp002723455	91.2019	826	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	88.4117	760	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	84.074	588	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661495.1	s__Pseudoalteromonas prydzensis	81.3823	527	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	-
GCF_012927645.1	s__Pseudoalteromonas arctica_A	81.3509	460	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238355.1	s__Pseudoalteromonas haloplanktis	81.176	529	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	81.0661	493	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	80.615	493	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	79.694	378	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	79.6747	400	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	79.665	357	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_018100905.1	s__Pseudoalteromonas sp018100905	79.2818	274	891	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:46:22,937] [INFO] GTDB search result was written to OceanDNA-b34950/result_gtdb.tsv
[2023-03-14 12:46:22,937] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:46:22,940] [INFO] DFAST_QC result json was written to OceanDNA-b34950/dqc_result.json
[2023-03-14 12:46:22,940] [INFO] DFAST_QC completed!
[2023-03-14 12:46:22,940] [INFO] Total running time: 0h1m36s