[2023-03-16 03:23:48,507] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference
[2023-03-16 03:23:50,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,645] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,645] [INFO] Running command: cat /var/lib/cwl/stgcd005544-01a6-47b8-8845-3fbd8aacf7e2/OceanDNA-b37593.fa | prodigal -d OceanDNA-b37593/cds.fna -a OceanDNA-b37593/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:19,066] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:19,067] [INFO] Task started: HMMsearch
[2023-03-16 03:24:19,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b37593/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference/reference_markers.hmm OceanDNA-b37593/protein.faa > /dev/null
[2023-03-16 03:24:19,336] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:19,337] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcd005544-01a6-47b8-8845-3fbd8aacf7e2/OceanDNA-b37593.fa]
[2023-03-16 03:24:19,364] [INFO] Query marker FASTA was written to OceanDNA-b37593/markers.fasta
[2023-03-16 03:24:19,365] [INFO] Task started: Blastn
[2023-03-16 03:24:19,365] [INFO] Running command: blastn -query OceanDNA-b37593/markers.fasta -db /var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference/reference_markers.fasta -out OceanDNA-b37593/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:19,976] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:19,977] [INFO] Selected 22 target genomes.
[2023-03-16 03:24:19,977] [INFO] Target genome list was writen to OceanDNA-b37593/target_genomes.txt
[2023-03-16 03:24:19,988] [INFO] Task started: fastANI
[2023-03-16 03:24:19,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd005544-01a6-47b8-8845-3fbd8aacf7e2/OceanDNA-b37593.fa --refList OceanDNA-b37593/target_genomes.txt --output OceanDNA-b37593/fastani_result.tsv --threads 1
[2023-03-16 03:24:34,499] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:34,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:34,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:34,509] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:34,509] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:34,509] [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
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.0632	195	1495	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.8359	189	1495	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.82	220	1495	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.7944	152	1495	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.6868	187	1495	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.6573	199	1495	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.6396	143	1495	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.5553	146	1495	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.5531	145	1495	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.5493	145	1495	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.3966	113	1495	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.1522	103	1495	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.1453	106	1495	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	75.662	50	1495	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	75.5934	57	1495	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:34,509] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37593/tc_result.tsv
[2023-03-16 03:24:34,509] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:34,509] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:34,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference/checkm_data
[2023-03-16 03:24:34,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:34,516] [INFO] Task started: CheckM
[2023-03-16 03:24:34,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37593/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37593/checkm_input OceanDNA-b37593/checkm_result
[2023-03-16 03:25:42,776] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:42,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:42,779] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:42,779] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:42,779] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37593/markers.fasta)
[2023-03-16 03:25:42,780] [INFO] Task started: Blastn
[2023-03-16 03:25:42,780] [INFO] Running command: blastn -query OceanDNA-b37593/markers.fasta -db /var/lib/cwl/stg74a94426-4459-4d90-971d-ffd45edac2e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37593/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:43,681] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:43,682] [INFO] Selected 14 target genomes.
[2023-03-16 03:25:43,682] [INFO] Target genome list was writen to OceanDNA-b37593/target_genomes_gtdb.txt
[2023-03-16 03:25:43,954] [INFO] Task started: fastANI
[2023-03-16 03:25:43,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd005544-01a6-47b8-8845-3fbd8aacf7e2/OceanDNA-b37593.fa --refList OceanDNA-b37593/target_genomes_gtdb.txt --output OceanDNA-b37593/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:54,719] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:54,728] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:25:54,728] [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	82.9259	1131	1495	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	78.1795	530	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCA_003646415.1	s__Halioglobus sp003646415	77.2625	141	1495	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	77.0632	195	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.9734	183	1495	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	76.9528	200	1495	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	76.863	294	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.8624	210	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.8598	158	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	76.8359	189	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.6573	199	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862985.1	s__Halioglobus sp002862985	76.5606	133	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480565.1	s__Halioglobus sp905480565	76.4406	73	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862465.1	s__Halioglobus sp002862465	76.1823	76	1495	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:54,728] [INFO] GTDB search result was written to OceanDNA-b37593/result_gtdb.tsv
[2023-03-16 03:25:54,728] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:54,730] [INFO] DFAST_QC result json was written to OceanDNA-b37593/dqc_result.json
[2023-03-16 03:25:54,730] [INFO] DFAST_QC completed!
[2023-03-16 03:25:54,730] [INFO] Total running time: 0h2m6s