[2023-03-19 03:10:00,770] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference
[2023-03-19 03:10:01,879] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,879] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,880] [INFO] Running command: cat /var/lib/cwl/stg8901f66e-cecd-4d1a-be3c-6da980a9879a/OceanDNA-b34946.fa | prodigal -d OceanDNA-b34946/cds.fna -a OceanDNA-b34946/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:17,211] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:17,211] [INFO] Task started: HMMsearch
[2023-03-19 03:10:17,211] [INFO] Running command: hmmsearch --tblout OceanDNA-b34946/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference/reference_markers.hmm OceanDNA-b34946/protein.faa > /dev/null
[2023-03-19 03:10:17,419] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:17,419] [INFO] Found 6/6 markers.
[2023-03-19 03:10:17,441] [INFO] Query marker FASTA was written to OceanDNA-b34946/markers.fasta
[2023-03-19 03:10:17,441] [INFO] Task started: Blastn
[2023-03-19 03:10:17,441] [INFO] Running command: blastn -query OceanDNA-b34946/markers.fasta -db /var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference/reference_markers.fasta -out OceanDNA-b34946/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:18,079] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:18,080] [INFO] Selected 12 target genomes.
[2023-03-19 03:10:18,080] [INFO] Target genome list was writen to OceanDNA-b34946/target_genomes.txt
[2023-03-19 03:10:18,087] [INFO] Task started: fastANI
[2023-03-19 03:10:18,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg8901f66e-cecd-4d1a-be3c-6da980a9879a/OceanDNA-b34946.fa --refList OceanDNA-b34946/target_genomes.txt --output OceanDNA-b34946/fastani_result.tsv --threads 1
[2023-03-19 03:10:27,820] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:27,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:27,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:27,827] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:27,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:10:27,827] [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 undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	94.8049	900	962	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	89.9375	861	962	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	89.8777	857	962	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	89.8295	869	962	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	89.7787	860	962	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	81.235	571	962	95	below_threshold
Pseudoalteromonas marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	81.1997	523	962	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.2289	478	962	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	79.8287	447	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:10:27,827] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34946/tc_result.tsv
[2023-03-19 03:10:27,827] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:27,827] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:27,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference/checkm_data
[2023-03-19 03:10:27,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:27,837] [INFO] Task started: CheckM
[2023-03-19 03:10:27,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34946/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34946/checkm_input OceanDNA-b34946/checkm_result
[2023-03-19 03:11:08,020] [INFO] Task succeeded: CheckM
[2023-03-19 03:11:08,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:11:08,023] [INFO] ===== Completeness check finished =====
[2023-03-19 03:11:08,023] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:11:08,023] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34946/markers.fasta)
[2023-03-19 03:11:08,024] [INFO] Task started: Blastn
[2023-03-19 03:11:08,024] [INFO] Running command: blastn -query OceanDNA-b34946/markers.fasta -db /var/lib/cwl/stg48df5057-3015-4786-839d-8127ef6c917f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34946/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:11:08,981] [INFO] Task succeeded: Blastn
[2023-03-19 03:11:08,982] [INFO] Selected 11 target genomes.
[2023-03-19 03:11:08,982] [INFO] Target genome list was writen to OceanDNA-b34946/target_genomes_gtdb.txt
[2023-03-19 03:11:09,056] [INFO] Task started: fastANI
[2023-03-19 03:11:09,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg8901f66e-cecd-4d1a-be3c-6da980a9879a/OceanDNA-b34946.fa --refList OceanDNA-b34946/target_genomes_gtdb.txt --output OceanDNA-b34946/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:11:18,637] [INFO] Task succeeded: fastANI
[2023-03-19 03:11:18,644] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:11:18,644] [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_000238275.3	s__Pseudoalteromonas undina	94.8049	900	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	94.0018	858	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	89.8295	869	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	87.6957	778	962	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	81.2875	570	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCA_000814675.1	s__Pseudoalteromonas distincta	81.2392	571	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_000238335.3	s__Pseudoalteromonas marina	81.2203	521	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	81.1346	556	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCA_007988745.1	s__Pseudoalteromonas atlantica	81.1201	558	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	-
GCF_014905615.1	s__Pseudoalteromonas aliena	81.0877	591	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	-
GCF_001661495.1	s__Pseudoalteromonas prydzensis	79.8218	448	962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-19 03:11:18,644] [INFO] GTDB search result was written to OceanDNA-b34946/result_gtdb.tsv
[2023-03-19 03:11:18,644] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:11:18,646] [INFO] DFAST_QC result json was written to OceanDNA-b34946/dqc_result.json
[2023-03-19 03:11:18,646] [INFO] DFAST_QC completed!
[2023-03-19 03:11:18,646] [INFO] Total running time: 0h1m18s