[2023-03-15 04:59:01,520] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:59:01,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:59:01,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference
[2023-03-15 04:59:03,420] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:59:03,421] [INFO] Task started: Prodigal
[2023-03-15 04:59:03,422] [INFO] Running command: cat /var/lib/cwl/stgde902f9c-5de9-41d5-9e5d-f1a49809eab8/OceanDNA-b37535.fa | prodigal -d OceanDNA-b37535/cds.fna -a OceanDNA-b37535/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:59:23,232] [INFO] Task succeeded: Prodigal
[2023-03-15 04:59:23,232] [INFO] Task started: HMMsearch
[2023-03-15 04:59:23,232] [INFO] Running command: hmmsearch --tblout OceanDNA-b37535/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference/reference_markers.hmm OceanDNA-b37535/protein.faa > /dev/null
[2023-03-15 04:59:23,439] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:59:23,440] [INFO] Found 6/6 markers.
[2023-03-15 04:59:23,517] [INFO] Query marker FASTA was written to OceanDNA-b37535/markers.fasta
[2023-03-15 04:59:23,517] [INFO] Task started: Blastn
[2023-03-15 04:59:23,517] [INFO] Running command: blastn -query OceanDNA-b37535/markers.fasta -db /var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference/reference_markers.fasta -out OceanDNA-b37535/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:59:24,181] [INFO] Task succeeded: Blastn
[2023-03-15 04:59:24,202] [INFO] Selected 19 target genomes.
[2023-03-15 04:59:24,203] [INFO] Target genome list was writen to OceanDNA-b37535/target_genomes.txt
[2023-03-15 04:59:24,215] [INFO] Task started: fastANI
[2023-03-15 04:59:24,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgde902f9c-5de9-41d5-9e5d-f1a49809eab8/OceanDNA-b37535.fa --refList OceanDNA-b37535/target_genomes.txt --output OceanDNA-b37535/fastani_result.tsv --threads 1
[2023-03-15 04:59:37,627] [INFO] Task succeeded: fastANI
[2023-03-15 04:59:37,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:59:37,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:59:37,635] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:59:37,635] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:59:37,635] [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
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	78.8176	475	1033	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	78.6803	480	1033	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.4601	211	1033	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.3262	181	1033	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.1252	185	1033	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.9929	208	1033	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.8481	166	1033	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.6942	99	1033	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.6733	102	1033	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	76.0787	53	1033	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	75.7018	51	1033	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:59:37,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37535/tc_result.tsv
[2023-03-15 04:59:37,657] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:59:37,657] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:59:37,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference/checkm_data
[2023-03-15 04:59:37,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:59:37,670] [INFO] Task started: CheckM
[2023-03-15 04:59:37,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37535/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37535/checkm_input OceanDNA-b37535/checkm_result
[2023-03-15 05:00:28,234] [INFO] Task succeeded: CheckM
[2023-03-15 05:00:28,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:00:28,434] [INFO] ===== Completeness check finished =====
[2023-03-15 05:00:28,434] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:00:28,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37535/markers.fasta)
[2023-03-15 05:00:28,435] [INFO] Task started: Blastn
[2023-03-15 05:00:28,435] [INFO] Running command: blastn -query OceanDNA-b37535/markers.fasta -db /var/lib/cwl/stgb33ece58-e174-41f8-9de6-aa766c584a98/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37535/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:29,546] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:29,575] [INFO] Selected 13 target genomes.
[2023-03-15 05:00:29,576] [INFO] Target genome list was writen to OceanDNA-b37535/target_genomes_gtdb.txt
[2023-03-15 05:00:29,638] [INFO] Task started: fastANI
[2023-03-15 05:00:29,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgde902f9c-5de9-41d5-9e5d-f1a49809eab8/OceanDNA-b37535.fa --refList OceanDNA-b37535/target_genomes_gtdb.txt --output OceanDNA-b37535/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:00:38,680] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:38,687] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:00:38,687] [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_000423125.1	s__Haliea salexigens	78.8269	474	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003719295.1	s__Haliea alexandrii	78.6761	480	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414665.1	s__Haliea sp002414665	78.5575	450	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCA_002416125.1	s__Haliea sp002416125	78.3416	452	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_002868715.1	s__Kineobactrum sediminis	77.4601	211	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	77.3284	180	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.1252	185	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	77.028	185	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.0124	188	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.9929	208	1033	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:00:38,696] [INFO] GTDB search result was written to OceanDNA-b37535/result_gtdb.tsv
[2023-03-15 05:00:38,713] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:00:38,726] [INFO] DFAST_QC result json was written to OceanDNA-b37535/dqc_result.json
[2023-03-15 05:00:38,726] [INFO] DFAST_QC completed!
[2023-03-15 05:00:38,726] [INFO] Total running time: 0h1m37s