[2023-03-15 09:48:16,575] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,575] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference
[2023-03-15 09:48:18,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,226] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,227] [INFO] Running command: cat /var/lib/cwl/stg5b2ff5b9-86dd-4730-8838-ecf515c11d57/OceanDNA-b41337.fa | prodigal -d OceanDNA-b41337/cds.fna -a OceanDNA-b41337/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:39,828] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:39,828] [INFO] Task started: HMMsearch
[2023-03-15 09:48:39,828] [INFO] Running command: hmmsearch --tblout OceanDNA-b41337/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference/reference_markers.hmm OceanDNA-b41337/protein.faa > /dev/null
[2023-03-15 09:48:40,045] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:40,046] [INFO] Found 6/6 markers.
[2023-03-15 09:48:40,070] [INFO] Query marker FASTA was written to OceanDNA-b41337/markers.fasta
[2023-03-15 09:48:40,070] [INFO] Task started: Blastn
[2023-03-15 09:48:40,070] [INFO] Running command: blastn -query OceanDNA-b41337/markers.fasta -db /var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference/reference_markers.fasta -out OceanDNA-b41337/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:40,755] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:40,756] [INFO] Selected 20 target genomes.
[2023-03-15 09:48:40,756] [INFO] Target genome list was writen to OceanDNA-b41337/target_genomes.txt
[2023-03-15 09:48:40,767] [INFO] Task started: fastANI
[2023-03-15 09:48:40,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2ff5b9-86dd-4730-8838-ecf515c11d57/OceanDNA-b41337.fa --refList OceanDNA-b41337/target_genomes.txt --output OceanDNA-b41337/fastani_result.tsv --threads 1
[2023-03-15 09:48:54,868] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:54,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:54,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:54,875] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:54,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:48:54,875] [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
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.7388	257	1172	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	78.3659	262	1172	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.9016	109	1172	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	77.8001	179	1172	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	76.8704	108	1172	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	76.0454	53	1172	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	75.9864	72	1172	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	75.5921	51	1172	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	75.4396	50	1172	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:48:54,875] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41337/tc_result.tsv
[2023-03-15 09:48:54,875] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:54,876] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:54,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference/checkm_data
[2023-03-15 09:48:54,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:54,883] [INFO] Task started: CheckM
[2023-03-15 09:48:54,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41337/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41337/checkm_input OceanDNA-b41337/checkm_result
[2023-03-15 09:49:50,017] [INFO] Task succeeded: CheckM
[2023-03-15 09:49:50,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:49:50,020] [INFO] ===== Completeness check finished =====
[2023-03-15 09:49:50,020] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:49:50,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41337/markers.fasta)
[2023-03-15 09:49:50,020] [INFO] Task started: Blastn
[2023-03-15 09:49:50,020] [INFO] Running command: blastn -query OceanDNA-b41337/markers.fasta -db /var/lib/cwl/stg45b99d3b-f021-4a22-9a12-446e23877e36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41337/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:49:51,162] [INFO] Task succeeded: Blastn
[2023-03-15 09:49:51,163] [INFO] Selected 20 target genomes.
[2023-03-15 09:49:51,163] [INFO] Target genome list was writen to OceanDNA-b41337/target_genomes_gtdb.txt
[2023-03-15 09:49:51,452] [INFO] Task started: fastANI
[2023-03-15 09:49:51,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2ff5b9-86dd-4730-8838-ecf515c11d57/OceanDNA-b41337.fa --refList OceanDNA-b41337/target_genomes_gtdb.txt --output OceanDNA-b41337/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:50:06,054] [INFO] Task succeeded: fastANI
[2023-03-15 09:50:06,063] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:50:06,064] [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
GCA_002723385.1	s__Oceanobacter sp002723385	99.729	960	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	99.82	99.82	0.84	0.84	2	conclusive
GCF_000422845.1	s__Oceanobacter kriegii	78.7218	258	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156675.1	s__Oleibacter marinus	77.9016	109	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002733205.1	s__UBA2009 sp002733205	77.7781	144	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_002314145.1	s__UBA2009 sp002314145	77.7777	135	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCF_007785795.1	s__UBA2009 sp002335285	77.7333	175	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002706025.1	s__UBA2009 sp002706025	77.6976	155	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCA_002331105.1	s__Oleibacter sp002331105	77.6741	93	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	-
GCA_016132445.1	s__UBA2009 sp016132445	77.3101	145	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCF_002237535.1	s__Bacterioplanes sanyensis_A	77.3095	115	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652515.1	s__Bacterioplanes sanyensis	76.8914	106	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bacterioplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	76.3813	84	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	76.2176	54	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	75.9803	71	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402255.1	s__Marinobacter sp018402255	75.9322	53	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:50:06,064] [INFO] GTDB search result was written to OceanDNA-b41337/result_gtdb.tsv
[2023-03-15 09:50:06,064] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:50:06,065] [INFO] DFAST_QC result json was written to OceanDNA-b41337/dqc_result.json
[2023-03-15 09:50:06,066] [INFO] DFAST_QC completed!
[2023-03-15 09:50:06,066] [INFO] Total running time: 0h1m49s