[2023-03-16 04:05:20,415] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference
[2023-03-16 04:05:22,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,132] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,132] [INFO] Running command: cat /var/lib/cwl/stg95dc699a-5ddf-4453-a99d-0aa5bf481b69/OceanDNA-b3564.fa | prodigal -d OceanDNA-b3564/cds.fna -a OceanDNA-b3564/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:45,716] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:45,716] [INFO] Task started: HMMsearch
[2023-03-16 04:05:45,716] [INFO] Running command: hmmsearch --tblout OceanDNA-b3564/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference/reference_markers.hmm OceanDNA-b3564/protein.faa > /dev/null
[2023-03-16 04:05:45,929] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:45,929] [INFO] Found 6/6 markers.
[2023-03-16 04:05:45,951] [INFO] Query marker FASTA was written to OceanDNA-b3564/markers.fasta
[2023-03-16 04:05:45,951] [INFO] Task started: Blastn
[2023-03-16 04:05:45,951] [INFO] Running command: blastn -query OceanDNA-b3564/markers.fasta -db /var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference/reference_markers.fasta -out OceanDNA-b3564/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:46,499] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:46,500] [INFO] Selected 13 target genomes.
[2023-03-16 04:05:46,500] [INFO] Target genome list was writen to OceanDNA-b3564/target_genomes.txt
[2023-03-16 04:05:46,506] [INFO] Task started: fastANI
[2023-03-16 04:05:46,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg95dc699a-5ddf-4453-a99d-0aa5bf481b69/OceanDNA-b3564.fa --refList OceanDNA-b3564/target_genomes.txt --output OceanDNA-b3564/fastani_result.tsv --threads 1
[2023-03-16 04:05:56,257] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:56,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:56,258] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:56,264] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:56,264] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:56,264] [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
Ancylomarina subtilis	strain=DSM 28825	GCA_004217115.1	1639035	1639035	type	True	81.0596	670	1218	95	below_threshold
Ancylomarina salipaludis	strain=SHSM-M15	GCA_004122035.1	2501299	2501299	type	True	80.7968	682	1218	95	below_threshold
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	78.2525	266	1218	95	below_threshold
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	77.8829	204	1218	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	77.6966	238	1218	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	77.6245	225	1218	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	77.5103	233	1218	95	below_threshold
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	77.4437	234	1218	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:56,265] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3564/tc_result.tsv
[2023-03-16 04:05:56,265] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:56,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:56,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference/checkm_data
[2023-03-16 04:05:56,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:56,271] [INFO] Task started: CheckM
[2023-03-16 04:05:56,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3564/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3564/checkm_input OceanDNA-b3564/checkm_result
[2023-03-16 04:06:55,669] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:55,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:55,672] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:55,672] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:55,672] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3564/markers.fasta)
[2023-03-16 04:06:55,672] [INFO] Task started: Blastn
[2023-03-16 04:06:55,672] [INFO] Running command: blastn -query OceanDNA-b3564/markers.fasta -db /var/lib/cwl/stg76881cc6-2ee5-48b3-b08f-738f3c77c24b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3564/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:56,434] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:56,435] [INFO] Selected 7 target genomes.
[2023-03-16 04:06:56,435] [INFO] Target genome list was writen to OceanDNA-b3564/target_genomes_gtdb.txt
[2023-03-16 04:06:56,442] [INFO] Task started: fastANI
[2023-03-16 04:06:56,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg95dc699a-5ddf-4453-a99d-0aa5bf481b69/OceanDNA-b3564.fa --refList OceanDNA-b3564/target_genomes_gtdb.txt --output OceanDNA-b3564/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:02,877] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:02,881] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:07:02,881] [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_016744515.1	s__Ancylomarina sp016744515	86.4792	760	1218	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009669305.1	s__Ancylomarina sp009669305	83.717	780	1218	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863355.1	s__Ancylomarina euxinus	82.8925	866	1218	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004217115.1	s__Ancylomarina subtilis	81.0504	671	1218	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122035.1	s__Ancylomarina salipaludis	80.8023	681	1218	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342745.1	s__Labilibaculum sp016342745	78.5137	284	1218	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:02,881] [INFO] GTDB search result was written to OceanDNA-b3564/result_gtdb.tsv
[2023-03-16 04:07:02,882] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:02,883] [INFO] DFAST_QC result json was written to OceanDNA-b3564/dqc_result.json
[2023-03-16 04:07:02,883] [INFO] DFAST_QC completed!
[2023-03-16 04:07:02,883] [INFO] Total running time: 0h1m42s