[2023-03-16 11:24:22,159] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:24:22,159] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:24:22,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference
[2023-03-16 11:24:24,990] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:24:24,991] [INFO] Task started: Prodigal
[2023-03-16 11:24:24,991] [INFO] Running command: cat /var/lib/cwl/stg3f6373cb-ad6d-4208-aa38-0d7f96267d24/OceanDNA-b36587.fa | prodigal -d OceanDNA-b36587/cds.fna -a OceanDNA-b36587/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:24:44,951] [INFO] Task succeeded: Prodigal
[2023-03-16 11:24:44,952] [INFO] Task started: HMMsearch
[2023-03-16 11:24:44,952] [INFO] Running command: hmmsearch --tblout OceanDNA-b36587/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference/reference_markers.hmm OceanDNA-b36587/protein.faa > /dev/null
[2023-03-16 11:24:45,142] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:24:45,143] [INFO] Found 6/6 markers.
[2023-03-16 11:24:45,161] [INFO] Query marker FASTA was written to OceanDNA-b36587/markers.fasta
[2023-03-16 11:24:45,162] [INFO] Task started: Blastn
[2023-03-16 11:24:45,162] [INFO] Running command: blastn -query OceanDNA-b36587/markers.fasta -db /var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference/reference_markers.fasta -out OceanDNA-b36587/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:24:45,879] [INFO] Task succeeded: Blastn
[2023-03-16 11:24:45,880] [INFO] Selected 13 target genomes.
[2023-03-16 11:24:45,880] [INFO] Target genome list was writen to OceanDNA-b36587/target_genomes.txt
[2023-03-16 11:24:45,888] [INFO] Task started: fastANI
[2023-03-16 11:24:45,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6373cb-ad6d-4208-aa38-0d7f96267d24/OceanDNA-b36587.fa --refList OceanDNA-b36587/target_genomes.txt --output OceanDNA-b36587/fastani_result.tsv --threads 1
[2023-03-16 11:24:56,265] [INFO] Task succeeded: fastANI
[2023-03-16 11:24:56,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:24:56,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:24:56,274] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:24:56,274] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:24:56,274] [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
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	82.7048	699	1008	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	81.6606	687	1008	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.73	586	1008	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	80.5499	590	1008	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	80.5415	583	1008	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	80.3438	566	1008	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.3649	373	1008	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.2469	294	1008	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.2477	224	1008	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	76.3781	78	1008	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.3475	91	1008	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.271	73	1008	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	76.148	95	1008	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:24:56,274] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36587/tc_result.tsv
[2023-03-16 11:24:56,274] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:24:56,274] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:24:56,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference/checkm_data
[2023-03-16 11:24:56,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:24:56,280] [INFO] Task started: CheckM
[2023-03-16 11:24:56,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36587/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36587/checkm_input OceanDNA-b36587/checkm_result
[2023-03-16 11:25:50,146] [INFO] Task succeeded: CheckM
[2023-03-16 11:25:50,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:25:50,151] [INFO] ===== Completeness check finished =====
[2023-03-16 11:25:50,151] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:25:50,151] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36587/markers.fasta)
[2023-03-16 11:25:50,153] [INFO] Task started: Blastn
[2023-03-16 11:25:50,153] [INFO] Running command: blastn -query OceanDNA-b36587/markers.fasta -db /var/lib/cwl/stg0fde963e-15d1-45fb-a552-b63ca3955641/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36587/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:25:52,305] [INFO] Task succeeded: Blastn
[2023-03-16 11:25:52,306] [INFO] Selected 10 target genomes.
[2023-03-16 11:25:52,306] [INFO] Target genome list was writen to OceanDNA-b36587/target_genomes_gtdb.txt
[2023-03-16 11:25:52,533] [INFO] Task started: fastANI
[2023-03-16 11:25:52,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6373cb-ad6d-4208-aa38-0d7f96267d24/OceanDNA-b36587.fa --refList OceanDNA-b36587/target_genomes_gtdb.txt --output OceanDNA-b36587/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:26:05,957] [INFO] Task succeeded: fastANI
[2023-03-16 11:26:05,963] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:26:05,964] [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_002733835.1	s__Alcanivorax sp002733835	97.396	894	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000155615.1	s__Alcanivorax sp000155615	92.4038	909	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCA_002726155.1	s__Alcanivorax sp002726155	90.6346	880	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009365.1	s__Alcanivorax borkumensis	82.6929	700	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.54	99.30	0.96	0.95	6	-
GCA_003862375.1	s__Alcanivorax jadensis_A	81.6748	675	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_000756655.1	s__Alcanivorax jadensis	81.6505	687	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_900107995.1	s__Alcanivorax sp900107995	81.4461	710	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.7092	588	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	80.666	619	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	80.5312	584	1008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:26:05,964] [INFO] GTDB search result was written to OceanDNA-b36587/result_gtdb.tsv
[2023-03-16 11:26:05,964] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:26:05,965] [INFO] DFAST_QC result json was written to OceanDNA-b36587/dqc_result.json
[2023-03-16 11:26:05,966] [INFO] DFAST_QC completed!
[2023-03-16 11:26:05,966] [INFO] Total running time: 0h1m44s