[2023-03-15 07:03:38,939] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference
[2023-03-15 07:03:40,098] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:40,098] [INFO] Task started: Prodigal
[2023-03-15 07:03:40,098] [INFO] Running command: cat /var/lib/cwl/stga371708f-f281-41a2-abde-4020749eca45/OceanDNA-b6569.fa | prodigal -d OceanDNA-b6569/cds.fna -a OceanDNA-b6569/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:59,183] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:59,183] [INFO] Task started: HMMsearch
[2023-03-15 07:03:59,183] [INFO] Running command: hmmsearch --tblout OceanDNA-b6569/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference/reference_markers.hmm OceanDNA-b6569/protein.faa > /dev/null
[2023-03-15 07:03:59,369] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:59,370] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga371708f-f281-41a2-abde-4020749eca45/OceanDNA-b6569.fa]
[2023-03-15 07:03:59,412] [INFO] Query marker FASTA was written to OceanDNA-b6569/markers.fasta
[2023-03-15 07:03:59,413] [INFO] Task started: Blastn
[2023-03-15 07:03:59,414] [INFO] Running command: blastn -query OceanDNA-b6569/markers.fasta -db /var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference/reference_markers.fasta -out OceanDNA-b6569/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:59,997] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:00,006] [INFO] Selected 22 target genomes.
[2023-03-15 07:04:00,007] [INFO] Target genome list was writen to OceanDNA-b6569/target_genomes.txt
[2023-03-15 07:04:00,017] [INFO] Task started: fastANI
[2023-03-15 07:04:00,017] [INFO] Running command: fastANI --query /var/lib/cwl/stga371708f-f281-41a2-abde-4020749eca45/OceanDNA-b6569.fa --refList OceanDNA-b6569/target_genomes.txt --output OceanDNA-b6569/fastani_result.tsv --threads 1
[2023-03-15 07:04:14,031] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:14,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:14,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:14,036] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 07:04:14,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 07:04:14,036] [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
Aureicoccus marinus	strain=SG-18	GCA_002954325.1	754435	754435	type	True	99.1442	767	791	95	conclusive
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.3921	50	791	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.2275	63	791	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.2263	63	791	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	75.9793	54	791	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	75.9793	54	791	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:04:14,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6569/tc_result.tsv
[2023-03-15 07:04:14,039] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:14,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:14,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference/checkm_data
[2023-03-15 07:04:14,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:14,053] [INFO] Task started: CheckM
[2023-03-15 07:04:14,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6569/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6569/checkm_input OceanDNA-b6569/checkm_result
[2023-03-15 07:05:04,267] [INFO] Task succeeded: CheckM
[2023-03-15 07:05:04,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.92%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:05:04,302] [INFO] ===== Completeness check finished =====
[2023-03-15 07:05:04,302] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:05:04,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6569/markers.fasta)
[2023-03-15 07:05:04,304] [INFO] Task started: Blastn
[2023-03-15 07:05:04,304] [INFO] Running command: blastn -query OceanDNA-b6569/markers.fasta -db /var/lib/cwl/stg4b5b1591-4498-4a62-a778-10f28f51dcfd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6569/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:05:05,194] [INFO] Task succeeded: Blastn
[2023-03-15 07:05:05,203] [INFO] Selected 21 target genomes.
[2023-03-15 07:05:05,203] [INFO] Target genome list was writen to OceanDNA-b6569/target_genomes_gtdb.txt
[2023-03-15 07:05:05,455] [INFO] Task started: fastANI
[2023-03-15 07:05:05,455] [INFO] Running command: fastANI --query /var/lib/cwl/stga371708f-f281-41a2-abde-4020749eca45/OceanDNA-b6569.fa --refList OceanDNA-b6569/target_genomes_gtdb.txt --output OceanDNA-b6569/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:05:18,207] [INFO] Task succeeded: fastANI
[2023-03-15 07:05:18,211] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:05:18,211] [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
GCF_002954325.1	s__Aureicoccus marinus	99.1442	767	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003385855.1	s__Muricauda sp003385855	76.252	50	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.2263	63	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584165.1	s__Muricauda sp003584165	76.0023	53	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001683915.1	s__Muricauda sp001683915	75.8308	55	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:05:18,215] [INFO] GTDB search result was written to OceanDNA-b6569/result_gtdb.tsv
[2023-03-15 07:05:18,217] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:05:18,220] [INFO] DFAST_QC result json was written to OceanDNA-b6569/dqc_result.json
[2023-03-15 07:05:18,220] [INFO] DFAST_QC completed!
[2023-03-15 07:05:18,220] [INFO] Total running time: 0h1m39s