[2023-03-16 08:22:25,421] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:25,422] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:25,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference
[2023-03-16 08:22:27,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:27,101] [INFO] Task started: Prodigal
[2023-03-16 08:22:27,102] [INFO] Running command: cat /var/lib/cwl/stg5fee07f4-ee25-4612-958f-676843d980cd/OceanDNA-b8089.fa | prodigal -d OceanDNA-b8089/cds.fna -a OceanDNA-b8089/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:35,209] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:35,209] [INFO] Task started: HMMsearch
[2023-03-16 08:22:35,209] [INFO] Running command: hmmsearch --tblout OceanDNA-b8089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference/reference_markers.hmm OceanDNA-b8089/protein.faa > /dev/null
[2023-03-16 08:22:35,390] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:35,391] [INFO] Found 6/6 markers.
[2023-03-16 08:22:35,416] [INFO] Query marker FASTA was written to OceanDNA-b8089/markers.fasta
[2023-03-16 08:22:35,416] [INFO] Task started: Blastn
[2023-03-16 08:22:35,416] [INFO] Running command: blastn -query OceanDNA-b8089/markers.fasta -db /var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference/reference_markers.fasta -out OceanDNA-b8089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:36,010] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:36,015] [INFO] Selected 31 target genomes.
[2023-03-16 08:22:36,016] [INFO] Target genome list was writen to OceanDNA-b8089/target_genomes.txt
[2023-03-16 08:22:36,034] [INFO] Task started: fastANI
[2023-03-16 08:22:36,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fee07f4-ee25-4612-958f-676843d980cd/OceanDNA-b8089.fa --refList OceanDNA-b8089/target_genomes.txt --output OceanDNA-b8089/fastani_result.tsv --threads 1
[2023-03-16 08:22:54,145] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:54,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:22:54,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:22:54,151] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:22:54,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:22:54,151] [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
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.481	73	449	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	75.4398	54	449	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	75.3511	52	449	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	75.349	52	449	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	75.289	51	449	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:22:54,153] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8089/tc_result.tsv
[2023-03-16 08:22:54,155] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:22:54,155] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:22:54,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference/checkm_data
[2023-03-16 08:22:54,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:22:54,223] [INFO] Task started: CheckM
[2023-03-16 08:22:54,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8089/checkm_input OceanDNA-b8089/checkm_result
[2023-03-16 08:23:19,488] [INFO] Task succeeded: CheckM
[2023-03-16 08:23:19,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.93%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:23:19,494] [INFO] ===== Completeness check finished =====
[2023-03-16 08:23:19,494] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:23:19,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8089/markers.fasta)
[2023-03-16 08:23:19,494] [INFO] Task started: Blastn
[2023-03-16 08:23:19,494] [INFO] Running command: blastn -query OceanDNA-b8089/markers.fasta -db /var/lib/cwl/stg9105db88-91d8-4c28-b2ba-8c1b089b65e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:23:20,475] [INFO] Task succeeded: Blastn
[2023-03-16 08:23:20,475] [INFO] Selected 8 target genomes.
[2023-03-16 08:23:20,476] [INFO] Target genome list was writen to OceanDNA-b8089/target_genomes_gtdb.txt
[2023-03-16 08:23:20,486] [INFO] Task started: fastANI
[2023-03-16 08:23:20,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fee07f4-ee25-4612-958f-676843d980cd/OceanDNA-b8089.fa --refList OceanDNA-b8089/target_genomes_gtdb.txt --output OceanDNA-b8089/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:23:23,286] [INFO] Task succeeded: fastANI
[2023-03-16 08:23:23,291] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:23:23,298] [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_902511755.1	s__MAG-121220-bin8 sp902511755	95.8193	333	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	conclusive
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	89.9295	365	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	86.8992	403	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	79.264	242	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	79.0672	296	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	78.9917	247	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	77.1509	121	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCF_002005425.1	s__Polaribacter sp002005425	75.1785	52	449	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:23:23,298] [INFO] GTDB search result was written to OceanDNA-b8089/result_gtdb.tsv
[2023-03-16 08:23:23,298] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:23:23,299] [INFO] DFAST_QC result json was written to OceanDNA-b8089/dqc_result.json
[2023-03-16 08:23:23,299] [INFO] DFAST_QC completed!
[2023-03-16 08:23:23,299] [INFO] Total running time: 0h0m58s