[2023-03-18 07:29:29,842] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,842] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,842] [INFO] DQC Reference Directory: /var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference
[2023-03-18 07:29:30,940] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,940] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,941] [INFO] Running command: cat /var/lib/cwl/stg760f90a7-8f6e-4304-9a71-1c111d7472ce/OceanDNA-b6567.fa | prodigal -d OceanDNA-b6567/cds.fna -a OceanDNA-b6567/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:51,515] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:51,516] [INFO] Task started: HMMsearch
[2023-03-18 07:29:51,516] [INFO] Running command: hmmsearch --tblout OceanDNA-b6567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference/reference_markers.hmm OceanDNA-b6567/protein.faa > /dev/null
[2023-03-18 07:29:51,688] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:51,688] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg760f90a7-8f6e-4304-9a71-1c111d7472ce/OceanDNA-b6567.fa]
[2023-03-18 07:29:51,706] [INFO] Query marker FASTA was written to OceanDNA-b6567/markers.fasta
[2023-03-18 07:29:51,707] [INFO] Task started: Blastn
[2023-03-18 07:29:51,707] [INFO] Running command: blastn -query OceanDNA-b6567/markers.fasta -db /var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference/reference_markers.fasta -out OceanDNA-b6567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:52,257] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:52,258] [INFO] Selected 21 target genomes.
[2023-03-18 07:29:52,258] [INFO] Target genome list was writen to OceanDNA-b6567/target_genomes.txt
[2023-03-18 07:29:52,267] [INFO] Task started: fastANI
[2023-03-18 07:29:52,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg760f90a7-8f6e-4304-9a71-1c111d7472ce/OceanDNA-b6567.fa --refList OceanDNA-b6567/target_genomes.txt --output OceanDNA-b6567/fastani_result.tsv --threads 1
[2023-03-18 07:30:05,367] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:05,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:05,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:05,374] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:05,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:05,374] [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	79.7243	392	797	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.6589	56	797	95	below_threshold
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	76.5922	61	797	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.3057	62	797	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	75.9996	71	797	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	75.9996	71	797	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	75.9972	61	797	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.9241	70	797	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	75.8538	53	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:05,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6567/tc_result.tsv
[2023-03-18 07:30:05,495] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:05,495] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:05,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference/checkm_data
[2023-03-18 07:30:05,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:05,518] [INFO] Task started: CheckM
[2023-03-18 07:30:05,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6567/checkm_input OceanDNA-b6567/checkm_result
[2023-03-18 07:30:59,175] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:59,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:59,177] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:59,178] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:59,178] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6567/markers.fasta)
[2023-03-18 07:30:59,178] [INFO] Task started: Blastn
[2023-03-18 07:30:59,178] [INFO] Running command: blastn -query OceanDNA-b6567/markers.fasta -db /var/lib/cwl/stge19a98de-72d5-442f-bda3-14281c6cea8b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:59,930] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:59,930] [INFO] Selected 22 target genomes.
[2023-03-18 07:30:59,931] [INFO] Target genome list was writen to OceanDNA-b6567/target_genomes_gtdb.txt
[2023-03-18 07:31:00,101] [INFO] Task started: fastANI
[2023-03-18 07:31:00,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg760f90a7-8f6e-4304-9a71-1c111d7472ce/OceanDNA-b6567.fa --refList OceanDNA-b6567/target_genomes_gtdb.txt --output OceanDNA-b6567/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:13,118] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:13,123] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:31:13,123] [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	79.7243	392	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	76.6589	56	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992675.1	s__Muricauda aquimarina	76.6281	60	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.3364	61	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584135.1	s__Muricauda sp003584135	76.0219	70	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003058265.1	s__Muricauda sp003058265	75.9972	61	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	75.9792	71	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_007785775.2	s__Muricauda sp003973595	75.9457	69	797	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:13,124] [INFO] GTDB search result was written to OceanDNA-b6567/result_gtdb.tsv
[2023-03-18 07:31:13,124] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:13,125] [INFO] DFAST_QC result json was written to OceanDNA-b6567/dqc_result.json
[2023-03-18 07:31:13,125] [INFO] DFAST_QC completed!
[2023-03-18 07:31:13,125] [INFO] Total running time: 0h1m43s