[2023-03-17 02:54:22,032] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:54:22,032] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:54:22,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference
[2023-03-17 02:54:23,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:54:23,266] [INFO] Task started: Prodigal
[2023-03-17 02:54:23,266] [INFO] Running command: cat /var/lib/cwl/stg8f882012-f33e-4d2c-a44a-9ae1953fd681/OceanDNA-b9835.fa | prodigal -d OceanDNA-b9835/cds.fna -a OceanDNA-b9835/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:54:32,360] [INFO] Task succeeded: Prodigal
[2023-03-17 02:54:32,360] [INFO] Task started: HMMsearch
[2023-03-17 02:54:32,360] [INFO] Running command: hmmsearch --tblout OceanDNA-b9835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference/reference_markers.hmm OceanDNA-b9835/protein.faa > /dev/null
[2023-03-17 02:54:32,548] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:54:32,548] [INFO] Found 6/6 markers.
[2023-03-17 02:54:32,566] [INFO] Query marker FASTA was written to OceanDNA-b9835/markers.fasta
[2023-03-17 02:54:32,566] [INFO] Task started: Blastn
[2023-03-17 02:54:32,566] [INFO] Running command: blastn -query OceanDNA-b9835/markers.fasta -db /var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference/reference_markers.fasta -out OceanDNA-b9835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:54:33,168] [INFO] Task succeeded: Blastn
[2023-03-17 02:54:33,171] [INFO] Selected 19 target genomes.
[2023-03-17 02:54:33,172] [INFO] Target genome list was writen to OceanDNA-b9835/target_genomes.txt
[2023-03-17 02:54:33,266] [INFO] Task started: fastANI
[2023-03-17 02:54:33,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f882012-f33e-4d2c-a44a-9ae1953fd681/OceanDNA-b9835.fa --refList OceanDNA-b9835/target_genomes.txt --output OceanDNA-b9835/fastani_result.tsv --threads 1
[2023-03-17 02:54:44,276] [INFO] Task succeeded: fastANI
[2023-03-17 02:54:44,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:54:44,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:54:44,287] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:54:44,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:54:44,287] [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 pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.7653	277	520	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.387	247	520	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	78.3762	248	520	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.2744	253	520	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	78.2258	273	520	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.2166	261	520	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.2117	273	520	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	78.1974	255	520	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.1711	260	520	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	78.1708	252	520	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.1693	255	520	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.1612	244	520	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	78.1444	254	520	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.1439	262	520	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	77.9724	257	520	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.8741	239	520	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.8105	246	520	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.7456	235	520	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.6964	243	520	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:54:44,289] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9835/tc_result.tsv
[2023-03-17 02:54:44,290] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:54:44,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:54:44,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference/checkm_data
[2023-03-17 02:54:44,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:54:44,305] [INFO] Task started: CheckM
[2023-03-17 02:54:44,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9835/checkm_input OceanDNA-b9835/checkm_result
[2023-03-17 02:55:11,369] [INFO] Task succeeded: CheckM
[2023-03-17 02:55:11,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:55:11,374] [INFO] ===== Completeness check finished =====
[2023-03-17 02:55:11,374] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:55:11,374] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9835/markers.fasta)
[2023-03-17 02:55:11,376] [INFO] Task started: Blastn
[2023-03-17 02:55:11,376] [INFO] Running command: blastn -query OceanDNA-b9835/markers.fasta -db /var/lib/cwl/stgeaa56e8c-7526-47cb-8ea1-bc6ed6781b5f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:55:12,365] [INFO] Task succeeded: Blastn
[2023-03-17 02:55:12,368] [INFO] Selected 22 target genomes.
[2023-03-17 02:55:12,368] [INFO] Target genome list was writen to OceanDNA-b9835/target_genomes_gtdb.txt
[2023-03-17 02:55:12,548] [INFO] Task started: fastANI
[2023-03-17 02:55:12,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f882012-f33e-4d2c-a44a-9ae1953fd681/OceanDNA-b9835.fa --refList OceanDNA-b9835/target_genomes_gtdb.txt --output OceanDNA-b9835/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:55:26,540] [INFO] Task succeeded: fastANI
[2023-03-17 02:55:26,552] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:55:26,552] [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_018663625.1	s__Polaribacter sp018663625	79.1439	303	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.23	98.14	0.90	0.83	5	-
GCF_000766795.1	s__Polaribacter sp000766795	78.8129	286	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	78.7582	278	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	78.7343	302	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	78.687	277	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608545.1	s__Polaribacter sp018608545	78.4965	198	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.39	97.39	0.93	0.93	2	-
GCF_900105145.1	s__Polaribacter sp900105145	78.4784	278	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	78.4396	262	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181765.1	s__Polaribacter sp905181765	78.4027	202	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_002954605.1	s__Polaribacter butkevichii	78.3773	247	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	78.3614	249	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	78.2798	249	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	78.2796	267	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCA_000981625.1	s__Polaribacter sp000981625	78.2662	216	520	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	78.2417	258	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014784055.1	s__Polaribacter haliotis	78.2394	272	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018861005.1	s__Polaribacter vadi_A	78.2266	274	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	78.2153	253	520	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	78.2118	251	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_019263805.1	s__Polaribacter sp011379025	78.1475	263	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002954685.1	s__Polaribacter porphyrae	77.8241	245	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	77.6922	244	520	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:55:26,552] [INFO] GTDB search result was written to OceanDNA-b9835/result_gtdb.tsv
[2023-03-17 02:55:26,553] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:55:26,555] [INFO] DFAST_QC result json was written to OceanDNA-b9835/dqc_result.json
[2023-03-17 02:55:26,555] [INFO] DFAST_QC completed!
[2023-03-17 02:55:26,555] [INFO] Total running time: 0h1m5s