[2023-03-15 05:56:37,374] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:56:37,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:56:37,392] [INFO] DQC Reference Directory: /var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference
[2023-03-15 05:56:39,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:56:39,381] [INFO] Task started: Prodigal
[2023-03-15 05:56:39,382] [INFO] Running command: cat /var/lib/cwl/stg21785e00-7872-4be3-844c-ede15a613a63/OceanDNA-b37596.fa | prodigal -d OceanDNA-b37596/cds.fna -a OceanDNA-b37596/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:57:03,619] [INFO] Task succeeded: Prodigal
[2023-03-15 05:57:03,619] [INFO] Task started: HMMsearch
[2023-03-15 05:57:03,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b37596/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference/reference_markers.hmm OceanDNA-b37596/protein.faa > /dev/null
[2023-03-15 05:57:03,847] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:57:03,847] [INFO] Found 6/6 markers.
[2023-03-15 05:57:04,003] [INFO] Query marker FASTA was written to OceanDNA-b37596/markers.fasta
[2023-03-15 05:57:04,005] [INFO] Task started: Blastn
[2023-03-15 05:57:04,005] [INFO] Running command: blastn -query OceanDNA-b37596/markers.fasta -db /var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference/reference_markers.fasta -out OceanDNA-b37596/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:57:04,684] [INFO] Task succeeded: Blastn
[2023-03-15 05:57:04,734] [INFO] Selected 23 target genomes.
[2023-03-15 05:57:04,734] [INFO] Target genome list was writen to OceanDNA-b37596/target_genomes.txt
[2023-03-15 05:57:04,748] [INFO] Task started: fastANI
[2023-03-15 05:57:04,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg21785e00-7872-4be3-844c-ede15a613a63/OceanDNA-b37596.fa --refList OceanDNA-b37596/target_genomes.txt --output OceanDNA-b37596/fastani_result.tsv --threads 1
[2023-03-15 05:57:19,080] [INFO] Task succeeded: fastANI
[2023-03-15 05:57:19,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:57:19,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:57:19,089] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:57:19,090] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:57:19,090] [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 sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.0116	190	1274	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.9619	172	1274	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.7743	187	1274	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.6875	165	1274	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.5813	131	1274	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	76.5632	76	1274	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.5555	174	1274	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.5534	134	1274	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.5478	136	1274	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.4776	133	1274	95	below_threshold
Pseudohalioglobus lutimaris	strain=HF004	GCA_002866825.1	1737061	1737061	type	True	76.2681	124	1274	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	75.6319	61	1274	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:57:19,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37596/tc_result.tsv
[2023-03-15 05:57:19,099] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:57:19,099] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:57:19,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference/checkm_data
[2023-03-15 05:57:19,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:57:19,108] [INFO] Task started: CheckM
[2023-03-15 05:57:19,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37596/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37596/checkm_input OceanDNA-b37596/checkm_result
[2023-03-15 05:58:19,332] [INFO] Task succeeded: CheckM
[2023-03-15 05:58:19,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:58:19,608] [INFO] ===== Completeness check finished =====
[2023-03-15 05:58:19,608] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:58:19,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37596/markers.fasta)
[2023-03-15 05:58:19,609] [INFO] Task started: Blastn
[2023-03-15 05:58:19,609] [INFO] Running command: blastn -query OceanDNA-b37596/markers.fasta -db /var/lib/cwl/stge8de98d9-480b-44c0-81fa-171afb78ad2e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37596/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:58:20,755] [INFO] Task succeeded: Blastn
[2023-03-15 05:58:20,763] [INFO] Selected 22 target genomes.
[2023-03-15 05:58:20,763] [INFO] Target genome list was writen to OceanDNA-b37596/target_genomes_gtdb.txt
[2023-03-15 05:58:20,779] [INFO] Task started: fastANI
[2023-03-15 05:58:20,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg21785e00-7872-4be3-844c-ede15a613a63/OceanDNA-b37596.fa --refList OceanDNA-b37596/target_genomes_gtdb.txt --output OceanDNA-b37596/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:58:36,256] [INFO] Task succeeded: fastANI
[2023-03-15 05:58:36,266] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:58:36,267] [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	78.7508	605	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	78.6696	575	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCA_002699145.1	s__Halioglobus sp002699145	77.1929	258	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_003646415.1	s__Halioglobus sp003646415	77.1915	146	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.0873	166	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.0241	192	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.0116	190	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862985.1	s__Halioglobus sp002862985	76.9129	116	1274	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	76.7743	187	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	76.7295	111	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.6903	149	1274	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	76.6875	165	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.6826	153	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.6336	182	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	76.5509	113	1274	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	76.5452	136	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_905480565.1	s__Halioglobus sp905480565	76.2761	77	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	75.6319	61	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112375.1	s__Pseudomonas citronellolis	75.4201	81	1274	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
--------------------------------------------------------------------------------
[2023-03-15 05:58:36,272] [INFO] GTDB search result was written to OceanDNA-b37596/result_gtdb.tsv
[2023-03-15 05:58:36,275] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:58:36,283] [INFO] DFAST_QC result json was written to OceanDNA-b37596/dqc_result.json
[2023-03-15 05:58:36,283] [INFO] DFAST_QC completed!
[2023-03-15 05:58:36,283] [INFO] Total running time: 0h1m59s