[2023-03-16 04:38:30,088] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,088] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference
[2023-03-16 04:38:31,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,205] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,205] [INFO] Running command: cat /var/lib/cwl/stg24e97fcc-23ec-45a2-959d-cf2dd464b5d7/OceanDNA-b10001.fa | prodigal -d OceanDNA-b10001/cds.fna -a OceanDNA-b10001/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:38:45,571] [INFO] Task succeeded: Prodigal
[2023-03-16 04:38:45,571] [INFO] Task started: HMMsearch
[2023-03-16 04:38:45,571] [INFO] Running command: hmmsearch --tblout OceanDNA-b10001/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference/reference_markers.hmm OceanDNA-b10001/protein.faa > /dev/null
[2023-03-16 04:38:45,768] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:38:45,768] [INFO] Found 6/6 markers.
[2023-03-16 04:38:45,784] [INFO] Query marker FASTA was written to OceanDNA-b10001/markers.fasta
[2023-03-16 04:38:45,785] [INFO] Task started: Blastn
[2023-03-16 04:38:45,785] [INFO] Running command: blastn -query OceanDNA-b10001/markers.fasta -db /var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference/reference_markers.fasta -out OceanDNA-b10001/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:38:46,453] [INFO] Task succeeded: Blastn
[2023-03-16 04:38:46,454] [INFO] Selected 15 target genomes.
[2023-03-16 04:38:46,454] [INFO] Target genome list was writen to OceanDNA-b10001/target_genomes.txt
[2023-03-16 04:38:46,501] [INFO] Task started: fastANI
[2023-03-16 04:38:46,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg24e97fcc-23ec-45a2-959d-cf2dd464b5d7/OceanDNA-b10001.fa --refList OceanDNA-b10001/target_genomes.txt --output OceanDNA-b10001/fastani_result.tsv --threads 1
[2023-03-16 04:38:56,215] [INFO] Task succeeded: fastANI
[2023-03-16 04:38:56,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:38:56,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:38:56,225] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:38:56,225] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:38:56,225] [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
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	80.9741	549	821	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.9271	548	821	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.9191	566	821	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.9067	571	821	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	80.906	554	821	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	80.8422	535	821	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	80.8265	530	821	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	80.5079	518	821	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.3047	537	821	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.3045	536	821	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	79.9869	507	821	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.3719	436	821	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	79.3389	473	821	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.5453	368	821	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.5368	349	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:38:56,225] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10001/tc_result.tsv
[2023-03-16 04:38:56,226] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:38:56,226] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:38:56,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference/checkm_data
[2023-03-16 04:38:56,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:38:56,230] [INFO] Task started: CheckM
[2023-03-16 04:38:56,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10001/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10001/checkm_input OceanDNA-b10001/checkm_result
[2023-03-16 04:39:34,779] [INFO] Task succeeded: CheckM
[2023-03-16 04:39:34,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:39:34,781] [INFO] ===== Completeness check finished =====
[2023-03-16 04:39:34,781] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:39:34,781] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10001/markers.fasta)
[2023-03-16 04:39:34,782] [INFO] Task started: Blastn
[2023-03-16 04:39:34,782] [INFO] Running command: blastn -query OceanDNA-b10001/markers.fasta -db /var/lib/cwl/stg9b53c25f-c994-40b0-9be8-52493771fec7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10001/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:35,861] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:35,862] [INFO] Selected 12 target genomes.
[2023-03-16 04:39:35,862] [INFO] Target genome list was writen to OceanDNA-b10001/target_genomes_gtdb.txt
[2023-03-16 04:39:35,869] [INFO] Task started: fastANI
[2023-03-16 04:39:35,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg24e97fcc-23ec-45a2-959d-cf2dd464b5d7/OceanDNA-b10001.fa --refList OceanDNA-b10001/target_genomes_gtdb.txt --output OceanDNA-b10001/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:39:44,174] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:44,181] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:39:44,181] [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_013373105.1	s__Polaribacter sp013373105	81.3495	511	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	80.9625	550	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	80.9409	564	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	80.8015	538	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018861005.1	s__Polaribacter vadi_A	80.7874	535	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	80.5298	522	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	80.5148	517	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	80.2795	539	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003129485.1	s__Polaribacter sp003129485	79.9932	506	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	79.5226	454	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	79.3385	473	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	79.2446	491	821	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:39:44,181] [INFO] GTDB search result was written to OceanDNA-b10001/result_gtdb.tsv
[2023-03-16 04:39:44,182] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:39:44,183] [INFO] DFAST_QC result json was written to OceanDNA-b10001/dqc_result.json
[2023-03-16 04:39:44,183] [INFO] DFAST_QC completed!
[2023-03-16 04:39:44,183] [INFO] Total running time: 0h1m14s