[2023-03-15 08:55:06,629] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,630] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference
[2023-03-15 08:55:08,346] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,347] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,347] [INFO] Running command: cat /var/lib/cwl/stg5b741aa4-97e0-4799-9b42-4aa132f487f6/OceanDNA-b1751.fa | prodigal -d OceanDNA-b1751/cds.fna -a OceanDNA-b1751/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:29,599] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:29,600] [INFO] Task started: HMMsearch
[2023-03-15 08:55:29,600] [INFO] Running command: hmmsearch --tblout OceanDNA-b1751/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference/reference_markers.hmm OceanDNA-b1751/protein.faa > /dev/null
[2023-03-15 08:55:29,907] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:29,907] [INFO] Found 6/6 markers.
[2023-03-15 08:55:29,940] [INFO] Query marker FASTA was written to OceanDNA-b1751/markers.fasta
[2023-03-15 08:55:29,941] [INFO] Task started: Blastn
[2023-03-15 08:55:29,941] [INFO] Running command: blastn -query OceanDNA-b1751/markers.fasta -db /var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference/reference_markers.fasta -out OceanDNA-b1751/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:30,647] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:30,648] [INFO] Selected 27 target genomes.
[2023-03-15 08:55:30,648] [INFO] Target genome list was writen to OceanDNA-b1751/target_genomes.txt
[2023-03-15 08:55:30,660] [INFO] Task started: fastANI
[2023-03-15 08:55:30,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b741aa4-97e0-4799-9b42-4aa132f487f6/OceanDNA-b1751.fa --refList OceanDNA-b1751/target_genomes.txt --output OceanDNA-b1751/fastani_result.tsv --threads 1
[2023-03-15 08:55:50,092] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:50,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:50,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:50,099] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:50,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:50,100] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.3136	103	1088	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.2118	104	1088	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.0117	69	1088	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.9499	88	1088	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9355	100	1088	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.926	90	1088	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	74.9424	71	1088	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	74.8928	52	1088	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:50,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1751/tc_result.tsv
[2023-03-15 08:55:50,100] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:50,100] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:50,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference/checkm_data
[2023-03-15 08:55:50,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:50,106] [INFO] Task started: CheckM
[2023-03-15 08:55:50,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1751/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1751/checkm_input OceanDNA-b1751/checkm_result
[2023-03-15 08:56:42,489] [INFO] Task succeeded: CheckM
[2023-03-15 08:56:42,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:56:42,492] [INFO] ===== Completeness check finished =====
[2023-03-15 08:56:42,492] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:56:42,493] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1751/markers.fasta)
[2023-03-15 08:56:42,494] [INFO] Task started: Blastn
[2023-03-15 08:56:42,494] [INFO] Running command: blastn -query OceanDNA-b1751/markers.fasta -db /var/lib/cwl/stg8e86956d-219a-4d81-bc39-f8f267dfd15e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1751/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:56:43,744] [INFO] Task succeeded: Blastn
[2023-03-15 08:56:43,745] [INFO] Selected 21 target genomes.
[2023-03-15 08:56:43,745] [INFO] Target genome list was writen to OceanDNA-b1751/target_genomes_gtdb.txt
[2023-03-15 08:56:43,821] [INFO] Task started: fastANI
[2023-03-15 08:56:43,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b741aa4-97e0-4799-9b42-4aa132f487f6/OceanDNA-b1751.fa --refList OceanDNA-b1751/target_genomes_gtdb.txt --output OceanDNA-b1751/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:55,006] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:55,016] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:55,017] [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_009937405.1	s__UBA11606 sp009937405	77.7571	158	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	-
GCA_018699415.1	s__UBA11606 sp018699415	77.6377	148	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.44	99.44	0.86	0.85	3	-
GCA_002694825.1	s__UBA11606 sp002694825	77.605	179	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_016845585.1	s__UBA11606 sp016845585	77.4016	239	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699625.1	s__UBA11606 sp002699625	77.3379	162	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480195.1	s__UBA11606 sp905480195	76.9532	132	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	76.7808	179	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_003231645.1	s__SZUA-87 sp003231645	76.4337	139	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__SZUA-87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852795.1	s__UBA11606 sp017852795	76.3836	105	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.3634	95	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009845995.1	s__VXYK01 sp009845995	76.3472	130	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VXYK01	95.0	99.45	99.19	0.95	0.93	8	-
GCA_016649895.1	s__Actinomarinicola sp016649895	76.2809	94	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658775.1	s__UBA3125 sp015658775	76.1155	69	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	-
GCA_009699605.1	s__WLNW01 sp009699605	76.034	89	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__WLNW01;g__WLNW01	95.0	99.58	99.52	0.88	0.87	4	-
GCA_014381745.1	s__UBA3125 sp014381745	75.9859	50	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.87	99.86	0.97	0.96	3	-
GCA_009843915.1	s__VYCW01 sp009843915	75.889	98	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	97.45	96.57	0.82	0.78	5	-
GCA_012730075.1	s__JAAYBP01 sp012730075	75.6772	73	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006515795.1	s__VFMC01 sp006515795	75.5896	56	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:55,017] [INFO] GTDB search result was written to OceanDNA-b1751/result_gtdb.tsv
[2023-03-15 08:56:55,017] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:55,018] [INFO] DFAST_QC result json was written to OceanDNA-b1751/dqc_result.json
[2023-03-15 08:56:55,019] [INFO] DFAST_QC completed!
[2023-03-15 08:56:55,019] [INFO] Total running time: 0h1m48s