[2023-03-18 03:59:27,752] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:27,752] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:27,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference
[2023-03-18 03:59:29,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:29,377] [INFO] Task started: Prodigal
[2023-03-18 03:59:29,377] [INFO] Running command: cat /var/lib/cwl/stg314300a7-9dc0-4eef-b31c-ba542f3c61ca/OceanDNA-b37603.fa | prodigal -d OceanDNA-b37603/cds.fna -a OceanDNA-b37603/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:55,392] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:55,392] [INFO] Task started: HMMsearch
[2023-03-18 03:59:55,392] [INFO] Running command: hmmsearch --tblout OceanDNA-b37603/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference/reference_markers.hmm OceanDNA-b37603/protein.faa > /dev/null
[2023-03-18 03:59:55,615] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:55,616] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg314300a7-9dc0-4eef-b31c-ba542f3c61ca/OceanDNA-b37603.fa]
[2023-03-18 03:59:55,642] [INFO] Query marker FASTA was written to OceanDNA-b37603/markers.fasta
[2023-03-18 03:59:55,642] [INFO] Task started: Blastn
[2023-03-18 03:59:55,642] [INFO] Running command: blastn -query OceanDNA-b37603/markers.fasta -db /var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference/reference_markers.fasta -out OceanDNA-b37603/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:56,269] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:56,270] [INFO] Selected 20 target genomes.
[2023-03-18 03:59:56,270] [INFO] Target genome list was writen to OceanDNA-b37603/target_genomes.txt
[2023-03-18 03:59:56,304] [INFO] Task started: fastANI
[2023-03-18 03:59:56,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg314300a7-9dc0-4eef-b31c-ba542f3c61ca/OceanDNA-b37603.fa --refList OceanDNA-b37603/target_genomes.txt --output OceanDNA-b37603/fastani_result.tsv --threads 1
[2023-03-18 04:00:09,124] [INFO] Task succeeded: fastANI
[2023-03-18 04:00:09,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:00:09,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:00:09,132] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:00:09,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:00:09,132] [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
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.3668	167	1392	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.0749	200	1392	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	77.0534	113	1392	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	77.0214	136	1392	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.013	151	1392	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.0075	166	1392	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.9732	116	1392	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.9225	124	1392	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.9097	116	1392	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.9007	116	1392	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.8999	178	1392	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.7412	120	1392	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:00:09,133] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37603/tc_result.tsv
[2023-03-18 04:00:09,133] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:00:09,133] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:00:09,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference/checkm_data
[2023-03-18 04:00:09,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:00:09,139] [INFO] Task started: CheckM
[2023-03-18 04:00:09,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37603/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37603/checkm_input OceanDNA-b37603/checkm_result
[2023-03-18 04:01:12,171] [INFO] Task succeeded: CheckM
[2023-03-18 04:01:12,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:01:12,174] [INFO] ===== Completeness check finished =====
[2023-03-18 04:01:12,174] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:01:12,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37603/markers.fasta)
[2023-03-18 04:01:12,174] [INFO] Task started: Blastn
[2023-03-18 04:01:12,174] [INFO] Running command: blastn -query OceanDNA-b37603/markers.fasta -db /var/lib/cwl/stgdd7ceb91-eedd-4551-a702-83a07e757aef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37603/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:01:13,166] [INFO] Task succeeded: Blastn
[2023-03-18 04:01:13,167] [INFO] Selected 18 target genomes.
[2023-03-18 04:01:13,167] [INFO] Target genome list was writen to OceanDNA-b37603/target_genomes_gtdb.txt
[2023-03-18 04:01:13,231] [INFO] Task started: fastANI
[2023-03-18 04:01:13,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg314300a7-9dc0-4eef-b31c-ba542f3c61ca/OceanDNA-b37603.fa --refList OceanDNA-b37603/target_genomes_gtdb.txt --output OceanDNA-b37603/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:01:25,823] [INFO] Task succeeded: fastANI
[2023-03-18 04:01:25,833] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:01:25,834] [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_902705825.1	s__Halioglobus japonicus_A	77.8287	161	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	77.3827	168	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646415.1	s__Halioglobus sp003646415	77.2825	128	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.0749	200	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.0536	197	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.0475	215	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	77.013	151	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.0099	165	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	76.9841	189	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.9727	115	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_000423125.1	s__Haliea salexigens	76.9254	124	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_008064635.1	s__Parahaliea aestuarii	76.9137	177	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.8114	148	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	76.7412	120	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.7218	145	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.6927	192	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_015222725.1	s__Halioglobus sp015222725	75.7621	76	1392	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:01:25,834] [INFO] GTDB search result was written to OceanDNA-b37603/result_gtdb.tsv
[2023-03-18 04:01:25,834] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:01:25,861] [INFO] DFAST_QC result json was written to OceanDNA-b37603/dqc_result.json
[2023-03-18 04:01:25,861] [INFO] DFAST_QC completed!
[2023-03-18 04:01:25,861] [INFO] Total running time: 0h1m58s