[2023-03-18 02:48:47,729] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:47,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:47,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference
[2023-03-18 02:48:49,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:49,547] [INFO] Task started: Prodigal
[2023-03-18 02:48:49,547] [INFO] Running command: cat /var/lib/cwl/stgbcfbd112-1651-4840-85a5-38ca2a60bb58/OceanDNA-b34714.fa | prodigal -d OceanDNA-b34714/cds.fna -a OceanDNA-b34714/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:49:08,841] [INFO] Task succeeded: Prodigal
[2023-03-18 02:49:08,842] [INFO] Task started: HMMsearch
[2023-03-18 02:49:08,842] [INFO] Running command: hmmsearch --tblout OceanDNA-b34714/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference/reference_markers.hmm OceanDNA-b34714/protein.faa > /dev/null
[2023-03-18 02:49:09,100] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:49:09,101] [INFO] Found 6/6 markers.
[2023-03-18 02:49:09,124] [INFO] Query marker FASTA was written to OceanDNA-b34714/markers.fasta
[2023-03-18 02:49:09,125] [INFO] Task started: Blastn
[2023-03-18 02:49:09,125] [INFO] Running command: blastn -query OceanDNA-b34714/markers.fasta -db /var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference/reference_markers.fasta -out OceanDNA-b34714/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:09,823] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:09,824] [INFO] Selected 17 target genomes.
[2023-03-18 02:49:09,824] [INFO] Target genome list was writen to OceanDNA-b34714/target_genomes.txt
[2023-03-18 02:49:09,839] [INFO] Task started: fastANI
[2023-03-18 02:49:09,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcfbd112-1651-4840-85a5-38ca2a60bb58/OceanDNA-b34714.fa --refList OceanDNA-b34714/target_genomes.txt --output OceanDNA-b34714/fastani_result.tsv --threads 1
[2023-03-18 02:49:22,061] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:22,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:22,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:22,069] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:22,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:49:22,069] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	80.3557	609	1197	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.2078	451	1197	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.1811	458	1197	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.9588	167	1197	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.7495	217	1197	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.7349	231	1197	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.5922	181	1197	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.5766	307	1197	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.4109	194	1197	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	76.9371	165	1197	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:49:22,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34714/tc_result.tsv
[2023-03-18 02:49:22,069] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:22,069] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:22,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference/checkm_data
[2023-03-18 02:49:22,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:22,076] [INFO] Task started: CheckM
[2023-03-18 02:49:22,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34714/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34714/checkm_input OceanDNA-b34714/checkm_result
[2023-03-18 02:50:11,047] [INFO] Task succeeded: CheckM
[2023-03-18 02:50:11,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:50:11,050] [INFO] ===== Completeness check finished =====
[2023-03-18 02:50:11,050] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:50:11,050] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34714/markers.fasta)
[2023-03-18 02:50:11,051] [INFO] Task started: Blastn
[2023-03-18 02:50:11,051] [INFO] Running command: blastn -query OceanDNA-b34714/markers.fasta -db /var/lib/cwl/stg4f6d9512-bb4f-4f60-bb0c-53d8e5b0bb02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34714/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:50:12,077] [INFO] Task succeeded: Blastn
[2023-03-18 02:50:12,077] [INFO] Selected 11 target genomes.
[2023-03-18 02:50:12,077] [INFO] Target genome list was writen to OceanDNA-b34714/target_genomes_gtdb.txt
[2023-03-18 02:50:12,156] [INFO] Task started: fastANI
[2023-03-18 02:50:12,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcfbd112-1651-4840-85a5-38ca2a60bb58/OceanDNA-b34714.fa --refList OceanDNA-b34714/target_genomes_gtdb.txt --output OceanDNA-b34714/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:50:21,688] [INFO] Task succeeded: fastANI
[2023-03-18 02:50:21,695] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:50:21,696] [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_003354085.1	s__Cognaticolwellia sp003354085	98.7901	1057	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002000025.1	s__Cognaticolwellia aestuarii	82.0021	778	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	81.2414	758	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	80.9789	663	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	80.7421	604	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	80.5385	613	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	80.5278	654	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	80.5273	670	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	80.434	629	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	80.386	599	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	80.3689	608	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:50:21,696] [INFO] GTDB search result was written to OceanDNA-b34714/result_gtdb.tsv
[2023-03-18 02:50:21,696] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:50:21,697] [INFO] DFAST_QC result json was written to OceanDNA-b34714/dqc_result.json
[2023-03-18 02:50:21,697] [INFO] DFAST_QC completed!
[2023-03-18 02:50:21,697] [INFO] Total running time: 0h1m34s