[2023-03-18 03:27:00,919] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,919] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference
[2023-03-18 03:27:02,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,637] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,637] [INFO] Running command: cat /var/lib/cwl/stgfb6b33bc-aefe-4e53-a774-615d75b98e45/OceanDNA-b270.fa | prodigal -d OceanDNA-b270/cds.fna -a OceanDNA-b270/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:22,504] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:22,505] [INFO] Task started: HMMsearch
[2023-03-18 03:27:22,505] [INFO] Running command: hmmsearch --tblout OceanDNA-b270/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference/reference_markers.hmm OceanDNA-b270/protein.faa > /dev/null
[2023-03-18 03:27:22,714] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:22,715] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfb6b33bc-aefe-4e53-a774-615d75b98e45/OceanDNA-b270.fa]
[2023-03-18 03:27:22,741] [INFO] Query marker FASTA was written to OceanDNA-b270/markers.fasta
[2023-03-18 03:27:22,742] [INFO] Task started: Blastn
[2023-03-18 03:27:22,742] [INFO] Running command: blastn -query OceanDNA-b270/markers.fasta -db /var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference/reference_markers.fasta -out OceanDNA-b270/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:23,359] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:23,359] [INFO] Selected 20 target genomes.
[2023-03-18 03:27:23,360] [INFO] Target genome list was writen to OceanDNA-b270/target_genomes.txt
[2023-03-18 03:27:23,371] [INFO] Task started: fastANI
[2023-03-18 03:27:23,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb6b33bc-aefe-4e53-a774-615d75b98e45/OceanDNA-b270.fa --refList OceanDNA-b270/target_genomes.txt --output OceanDNA-b270/fastani_result.tsv --threads 1
[2023-03-18 03:27:36,517] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:36,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:36,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:36,522] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:36,522] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:36,522] [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
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.659	65	1095	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	74.6318	50	1095	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	74.6101	80	1095	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:36,522] [INFO] DFAST Taxonomy check result was written to OceanDNA-b270/tc_result.tsv
[2023-03-18 03:27:36,522] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:36,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:36,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference/checkm_data
[2023-03-18 03:27:36,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:36,528] [INFO] Task started: CheckM
[2023-03-18 03:27:36,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b270/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b270/checkm_input OceanDNA-b270/checkm_result
[2023-03-18 03:28:26,126] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:26,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:26,129] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:26,130] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:26,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b270/markers.fasta)
[2023-03-18 03:28:26,130] [INFO] Task started: Blastn
[2023-03-18 03:28:26,130] [INFO] Running command: blastn -query OceanDNA-b270/markers.fasta -db /var/lib/cwl/stg39d77c37-2866-449f-84e3-701fc1d8e023/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b270/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:27,126] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:27,127] [INFO] Selected 23 target genomes.
[2023-03-18 03:28:27,127] [INFO] Target genome list was writen to OceanDNA-b270/target_genomes_gtdb.txt
[2023-03-18 03:28:27,146] [INFO] Task started: fastANI
[2023-03-18 03:28:27,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb6b33bc-aefe-4e53-a774-615d75b98e45/OceanDNA-b270.fa --refList OceanDNA-b270/target_genomes_gtdb.txt --output OceanDNA-b270/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:28:42,299] [INFO] Task succeeded: fastANI
[2023-03-18 03:28:42,310] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:28:42,310] [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_002346545.1	s__UBA2994 sp002346545	81.0148	653	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA2994	95.0	99.87	99.87	0.91	0.91	2	-
GCA_015659035.1	s__NP936 sp015659035	77.239	302	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009861545.1	s__WTFV01 sp009861545	76.7526	280	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_011523485.1	s__WTFV01 sp011523485	76.3282	182	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730525.1	s__UBA2161 sp002730525	76.2722	96	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.1382	110	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_016184105.1	s__JACPDI01 sp016184105	76.0088	83	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACPDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003533545.1	s__UBA9620 sp003533545	75.9675	95	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__UBA9620	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695405.1	s__Luteitalea sp013695405	75.8495	72	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464065.1	s__Luteitalea sp001464065	75.8147	114	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883165.1	s__JADGOC01 sp017883165	75.753	79	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	75.6878	115	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213695.1	s__Gp6-AA40 sp016213695	75.6271	101	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767455.1	s__2-12-FULL-66-21 sp001767455	75.5756	98	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	-
GCA_003223835.1	s__Gp6-AA38 sp003223835	75.5621	76	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__Gp6-AA38	95.0	98.48	98.48	0.89	0.89	2	-
GCA_902826065.1	s__CADEFD01 sp902826065	75.5274	131	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789705.1	s__CADEFD01 sp016789705	75.3937	113	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	75.3567	78	1095	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:28:42,310] [INFO] GTDB search result was written to OceanDNA-b270/result_gtdb.tsv
[2023-03-18 03:28:42,310] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:28:42,312] [INFO] DFAST_QC result json was written to OceanDNA-b270/dqc_result.json
[2023-03-18 03:28:42,312] [INFO] DFAST_QC completed!
[2023-03-18 03:28:42,312] [INFO] Total running time: 0h1m41s