[2023-03-18 22:16:20,362] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:16:20,362] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:16:20,362] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference
[2023-03-18 22:16:21,460] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:16:21,460] [INFO] Task started: Prodigal
[2023-03-18 22:16:21,461] [INFO] Running command: cat /var/lib/cwl/stg6357a282-5994-4ec6-a160-74236171764a/OceanDNA-b34242.fa | prodigal -d OceanDNA-b34242/cds.fna -a OceanDNA-b34242/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:16:30,347] [INFO] Task succeeded: Prodigal
[2023-03-18 22:16:30,347] [INFO] Task started: HMMsearch
[2023-03-18 22:16:30,347] [INFO] Running command: hmmsearch --tblout OceanDNA-b34242/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference/reference_markers.hmm OceanDNA-b34242/protein.faa > /dev/null
[2023-03-18 22:16:30,510] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:16:30,511] [INFO] Found 6/6 markers.
[2023-03-18 22:16:30,528] [INFO] Query marker FASTA was written to OceanDNA-b34242/markers.fasta
[2023-03-18 22:16:30,529] [INFO] Task started: Blastn
[2023-03-18 22:16:30,529] [INFO] Running command: blastn -query OceanDNA-b34242/markers.fasta -db /var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference/reference_markers.fasta -out OceanDNA-b34242/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:16:31,301] [INFO] Task succeeded: Blastn
[2023-03-18 22:16:31,303] [INFO] Selected 28 target genomes.
[2023-03-18 22:16:31,303] [INFO] Target genome list was writen to OceanDNA-b34242/target_genomes.txt
[2023-03-18 22:16:31,322] [INFO] Task started: fastANI
[2023-03-18 22:16:31,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg6357a282-5994-4ec6-a160-74236171764a/OceanDNA-b34242.fa --refList OceanDNA-b34242/target_genomes.txt --output OceanDNA-b34242/fastani_result.tsv --threads 1
[2023-03-18 22:16:46,995] [INFO] Task succeeded: fastANI
[2023-03-18 22:16:46,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:16:46,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:16:47,007] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:16:47,007] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:16:47,007] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.5215	75	320	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.471	84	320	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.4333	84	320	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	77.3107	81	320	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.9371	69	320	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8564	69	320	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.8418	65	320	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.8227	80	320	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.644	57	320	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.5639	63	320	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.535	54	320	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	76.5018	59	320	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.4076	54	320	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.2788	56	320	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	76.2399	54	320	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.1344	63	320	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	76.0193	58	320	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	75.9819	50	320	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	75.7921	56	320	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:16:47,008] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34242/tc_result.tsv
[2023-03-18 22:16:47,008] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:16:47,008] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:16:47,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference/checkm_data
[2023-03-18 22:16:47,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:16:47,013] [INFO] Task started: CheckM
[2023-03-18 22:16:47,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34242/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34242/checkm_input OceanDNA-b34242/checkm_result
[2023-03-18 22:17:12,525] [INFO] Task succeeded: CheckM
[2023-03-18 22:17:12,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:17:12,527] [INFO] ===== Completeness check finished =====
[2023-03-18 22:17:12,527] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:17:12,528] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34242/markers.fasta)
[2023-03-18 22:17:12,529] [INFO] Task started: Blastn
[2023-03-18 22:17:12,529] [INFO] Running command: blastn -query OceanDNA-b34242/markers.fasta -db /var/lib/cwl/stgdb91a80a-1880-4ac5-a879-7462ceb0b78c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34242/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:13,893] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:13,894] [INFO] Selected 23 target genomes.
[2023-03-18 22:17:13,894] [INFO] Target genome list was writen to OceanDNA-b34242/target_genomes_gtdb.txt
[2023-03-18 22:17:13,914] [INFO] Task started: fastANI
[2023-03-18 22:17:13,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg6357a282-5994-4ec6-a160-74236171764a/OceanDNA-b34242.fa --refList OceanDNA-b34242/target_genomes_gtdb.txt --output OceanDNA-b34242/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:17:25,762] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:25,772] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:17:25,772] [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_000801295.1	s__MONJU sp000801295	78.8667	147	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002009425.1	s__41T-STBD-0c-01a sp002009425	78.2165	122	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__41T-STBD-0c-01a	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	77.5215	75	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696905.1	s__MONJU sp003696905	77.3365	89	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.2288	76	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_003562815.1	s__Halochromatium sp003562815	77.0376	50	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCA_015231665.1	s__JADGBD01 sp015231665	77.0223	56	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.9784	79	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276755.1	s__Marichromatium bheemlicum	76.9371	69	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.8418	65	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009497875.2	s__JADGBD01 sp009497875	76.7909	73	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972985.1	s__Thiolapillus sp003972985	76.7229	66	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	76.5559	56	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_000377785.1	s__Thioalkalivibrio sp000377785	76.5469	50	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	76.2231	58	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	76.1836	56	320	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-18 22:17:25,773] [INFO] GTDB search result was written to OceanDNA-b34242/result_gtdb.tsv
[2023-03-18 22:17:25,773] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:17:25,775] [INFO] DFAST_QC result json was written to OceanDNA-b34242/dqc_result.json
[2023-03-18 22:17:25,775] [INFO] DFAST_QC completed!
[2023-03-18 22:17:25,775] [INFO] Total running time: 0h1m5s