[2023-03-19 04:29:37,746] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,746] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference
[2023-03-19 04:29:38,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stg05be05ea-a15d-4a2e-ba64-ab7903bafe30/OceanDNA-b286.fa | prodigal -d OceanDNA-b286/cds.fna -a OceanDNA-b286/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:30:03,606] [INFO] Task succeeded: Prodigal
[2023-03-19 04:30:03,606] [INFO] Task started: HMMsearch
[2023-03-19 04:30:03,606] [INFO] Running command: hmmsearch --tblout OceanDNA-b286/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference/reference_markers.hmm OceanDNA-b286/protein.faa > /dev/null
[2023-03-19 04:30:03,824] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:03,824] [INFO] Found 6/6 markers.
[2023-03-19 04:30:03,852] [INFO] Query marker FASTA was written to OceanDNA-b286/markers.fasta
[2023-03-19 04:30:03,852] [INFO] Task started: Blastn
[2023-03-19 04:30:03,852] [INFO] Running command: blastn -query OceanDNA-b286/markers.fasta -db /var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference/reference_markers.fasta -out OceanDNA-b286/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:04,401] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:04,402] [INFO] Selected 30 target genomes.
[2023-03-19 04:30:04,402] [INFO] Target genome list was writen to OceanDNA-b286/target_genomes.txt
[2023-03-19 04:30:04,418] [INFO] Task started: fastANI
[2023-03-19 04:30:04,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg05be05ea-a15d-4a2e-ba64-ab7903bafe30/OceanDNA-b286.fa --refList OceanDNA-b286/target_genomes.txt --output OceanDNA-b286/fastani_result.tsv --threads 1
[2023-03-19 04:30:23,518] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:23,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:23,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:23,522] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:23,522] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:23,522] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.4736	97	1320	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	74.8227	52	1320	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.6544	70	1320	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:23,522] [INFO] DFAST Taxonomy check result was written to OceanDNA-b286/tc_result.tsv
[2023-03-19 04:30:23,522] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:23,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:23,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference/checkm_data
[2023-03-19 04:30:23,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:23,529] [INFO] Task started: CheckM
[2023-03-19 04:30:23,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b286/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b286/checkm_input OceanDNA-b286/checkm_result
[2023-03-19 04:31:24,342] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:24,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:24,346] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:24,346] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:24,346] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b286/markers.fasta)
[2023-03-19 04:31:24,348] [INFO] Task started: Blastn
[2023-03-19 04:31:24,348] [INFO] Running command: blastn -query OceanDNA-b286/markers.fasta -db /var/lib/cwl/stgdc9f3bea-76d6-4280-b8e8-fd0d08e7d18f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b286/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:25,151] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:25,151] [INFO] Selected 19 target genomes.
[2023-03-19 04:31:25,152] [INFO] Target genome list was writen to OceanDNA-b286/target_genomes_gtdb.txt
[2023-03-19 04:31:25,230] [INFO] Task started: fastANI
[2023-03-19 04:31:25,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg05be05ea-a15d-4a2e-ba64-ab7903bafe30/OceanDNA-b286.fa --refList OceanDNA-b286/target_genomes_gtdb.txt --output OceanDNA-b286/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:38,944] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:38,952] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:31:38,953] [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_002712885.1	s__UBA8438 sp002712885	92.7239	961	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778315.1	s__UBA8438 sp005778315	78.258	404	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA8438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015659035.1	s__NP936 sp015659035	77.8183	360	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726085.1	s__NP936 sp002726085	77.5958	420	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533545.1	s__UBA9620 sp003533545	76.6918	146	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346545.1	s__UBA2994 sp002346545	76.6142	254	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_009861545.1	s__WTFV01 sp009861545	76.5566	272	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_002328835.1	s__UBA2161 sp002328835	76.1519	112	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_016871255.1	s__VFZH01 sp016871255	75.7529	100	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767195.1	s__Gp6-AA40 sp001767195	75.6604	71	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.78	99.78	0.93	0.93	2	-
GCA_009380045.1	s__WHSN01 sp009380045	75.6596	71	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195265.1	s__Gp6-AA45 sp016195265	75.6433	94	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	75.4782	87	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
GCA_003170135.1	s__Fen-181 sp003170135	75.4038	74	1320	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:38,953] [INFO] GTDB search result was written to OceanDNA-b286/result_gtdb.tsv
[2023-03-19 04:31:38,953] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:38,954] [INFO] DFAST_QC result json was written to OceanDNA-b286/dqc_result.json
[2023-03-19 04:31:38,954] [INFO] DFAST_QC completed!
[2023-03-19 04:31:38,954] [INFO] Total running time: 0h2m1s