[2023-03-15 20:34:26,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,739] [INFO] DQC Reference Directory: /var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference
[2023-03-15 20:34:28,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,462] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,462] [INFO] Running command: cat /var/lib/cwl/stg7fddbc4a-d9fb-4f4f-9218-6f14ec8132ad/OceanDNA-b38177.fa | prodigal -d OceanDNA-b38177/cds.fna -a OceanDNA-b38177/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:47,426] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:47,427] [INFO] Task started: HMMsearch
[2023-03-15 20:34:47,427] [INFO] Running command: hmmsearch --tblout OceanDNA-b38177/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference/reference_markers.hmm OceanDNA-b38177/protein.faa > /dev/null
[2023-03-15 20:34:47,625] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:47,626] [INFO] Found 6/6 markers.
[2023-03-15 20:34:47,648] [INFO] Query marker FASTA was written to OceanDNA-b38177/markers.fasta
[2023-03-15 20:34:47,648] [INFO] Task started: Blastn
[2023-03-15 20:34:47,648] [INFO] Running command: blastn -query OceanDNA-b38177/markers.fasta -db /var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference/reference_markers.fasta -out OceanDNA-b38177/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:48,522] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:48,523] [INFO] Selected 18 target genomes.
[2023-03-15 20:34:48,524] [INFO] Target genome list was writen to OceanDNA-b38177/target_genomes.txt
[2023-03-15 20:34:48,532] [INFO] Task started: fastANI
[2023-03-15 20:34:48,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fddbc4a-d9fb-4f4f-9218-6f14ec8132ad/OceanDNA-b38177.fa --refList OceanDNA-b38177/target_genomes.txt --output OceanDNA-b38177/fastani_result.tsv --threads 1
[2023-03-15 20:35:02,285] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:02,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:02,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:02,296] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:02,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 20:35:02,296] [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
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	84.0682	691	1049	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.2608	312	1049	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	78.1481	310	1049	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	78.1297	273	1049	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	77.8936	299	1049	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	77.8246	309	1049	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.6417	267	1049	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	77.4182	218	1049	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.344	226	1049	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.1508	217	1049	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.0785	171	1049	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.9283	187	1049	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.8588	183	1049	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.8476	138	1049	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.6736	205	1049	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	76.5453	124	1049	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	76.4674	133	1049	95	below_threshold
Pseudomonas typographi	strain=CA3A	GCA_014694385.1	2715964	2715964	type	True	75.3777	90	1049	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 20:35:02,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38177/tc_result.tsv
[2023-03-15 20:35:02,297] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:02,297] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:02,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference/checkm_data
[2023-03-15 20:35:02,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:02,302] [INFO] Task started: CheckM
[2023-03-15 20:35:02,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38177/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38177/checkm_input OceanDNA-b38177/checkm_result
[2023-03-15 20:35:50,003] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:50,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:50,006] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:50,006] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:50,006] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38177/markers.fasta)
[2023-03-15 20:35:50,007] [INFO] Task started: Blastn
[2023-03-15 20:35:50,007] [INFO] Running command: blastn -query OceanDNA-b38177/markers.fasta -db /var/lib/cwl/stge905283c-ed56-406f-9e37-a01423f1f8a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38177/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:51,574] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:51,575] [INFO] Selected 18 target genomes.
[2023-03-15 20:35:51,575] [INFO] Target genome list was writen to OceanDNA-b38177/target_genomes_gtdb.txt
[2023-03-15 20:35:51,871] [INFO] Task started: fastANI
[2023-03-15 20:35:51,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fddbc4a-d9fb-4f4f-9218-6f14ec8132ad/OceanDNA-b38177.fa --refList OceanDNA-b38177/target_genomes_gtdb.txt --output OceanDNA-b38177/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:36:05,599] [INFO] Task succeeded: fastANI
[2023-03-15 20:36:05,610] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:36:05,610] [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_000764025.1	s__Pseudohaliea rubra	84.0464	693	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	78.6994	373	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	78.6441	329	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_004745945.1	s__Halioglobus sp004745945	78.6256	368	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	78.4621	304	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_003402235.1	s__Parahaliea mediterranea	78.2589	311	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	78.1835	307	1049	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	78.1574	271	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340525.1	s__Chromatocurvus halotolerans	77.823	308	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_009937575.1	s__Halioglobus sp009937575	77.6713	203	1049	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	77.6417	267	1049	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	77.4044	219	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	77.3194	228	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_004354085.1	s__Halioglobus sp004354085	77.0785	171	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.8452	184	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961645.1	s__BRH-c0 sp000961645	76.8152	60	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633775.1	s__Kushneria sinocarnis	76.2554	86	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694385.1	s__Pseudomonas_E typographi	75.3777	90	1049	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.61	99.56	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-15 20:36:05,610] [INFO] GTDB search result was written to OceanDNA-b38177/result_gtdb.tsv
[2023-03-15 20:36:05,610] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:36:05,612] [INFO] DFAST_QC result json was written to OceanDNA-b38177/dqc_result.json
[2023-03-15 20:36:05,612] [INFO] DFAST_QC completed!
[2023-03-15 20:36:05,612] [INFO] Total running time: 0h1m39s