[2023-03-17 10:08:39,128] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,128] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,128] [INFO] DQC Reference Directory: /var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference
[2023-03-17 10:08:40,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,227] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,227] [INFO] Running command: cat /var/lib/cwl/stg3f977d57-1b91-4d97-aa1d-f4ce82946315/OceanDNA-b12001.fa | prodigal -d OceanDNA-b12001/cds.fna -a OceanDNA-b12001/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:09:06,038] [INFO] Task succeeded: Prodigal
[2023-03-17 10:09:06,038] [INFO] Task started: HMMsearch
[2023-03-17 10:09:06,038] [INFO] Running command: hmmsearch --tblout OceanDNA-b12001/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference/reference_markers.hmm OceanDNA-b12001/protein.faa > /dev/null
[2023-03-17 10:09:06,213] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:09:06,213] [INFO] Found 6/6 markers.
[2023-03-17 10:09:06,228] [INFO] Query marker FASTA was written to OceanDNA-b12001/markers.fasta
[2023-03-17 10:09:06,229] [INFO] Task started: Blastn
[2023-03-17 10:09:06,229] [INFO] Running command: blastn -query OceanDNA-b12001/markers.fasta -db /var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference/reference_markers.fasta -out OceanDNA-b12001/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:06,799] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:06,800] [INFO] Selected 31 target genomes.
[2023-03-17 10:09:06,800] [INFO] Target genome list was writen to OceanDNA-b12001/target_genomes.txt
[2023-03-17 10:09:06,882] [INFO] Task started: fastANI
[2023-03-17 10:09:06,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f977d57-1b91-4d97-aa1d-f4ce82946315/OceanDNA-b12001.fa --refList OceanDNA-b12001/target_genomes.txt --output OceanDNA-b12001/fastani_result.tsv --threads 1
[2023-03-17 10:09:24,737] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:24,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:09:24,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:09:24,738] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:09:24,738] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:09:24,738] [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
--------------------------------------------------------------------------------
[2023-03-17 10:09:24,738] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12001/tc_result.tsv
[2023-03-17 10:09:24,739] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:09:24,739] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:09:24,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference/checkm_data
[2023-03-17 10:09:24,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:09:24,746] [INFO] Task started: CheckM
[2023-03-17 10:09:24,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12001/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12001/checkm_input OceanDNA-b12001/checkm_result
[2023-03-17 10:10:33,095] [INFO] Task succeeded: CheckM
[2023-03-17 10:10:33,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:10:33,184] [INFO] ===== Completeness check finished =====
[2023-03-17 10:10:33,184] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:10:33,185] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12001/markers.fasta)
[2023-03-17 10:10:33,186] [INFO] Task started: Blastn
[2023-03-17 10:10:33,186] [INFO] Running command: blastn -query OceanDNA-b12001/markers.fasta -db /var/lib/cwl/stga5d4768f-6dde-478b-ad2f-991cc600b150/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12001/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:10:33,992] [INFO] Task succeeded: Blastn
[2023-03-17 10:10:33,995] [INFO] Selected 17 target genomes.
[2023-03-17 10:10:33,995] [INFO] Target genome list was writen to OceanDNA-b12001/target_genomes_gtdb.txt
[2023-03-17 10:10:34,031] [INFO] Task started: fastANI
[2023-03-17 10:10:34,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f977d57-1b91-4d97-aa1d-f4ce82946315/OceanDNA-b12001.fa --refList OceanDNA-b12001/target_genomes_gtdb.txt --output OceanDNA-b12001/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:10:42,558] [INFO] Task succeeded: fastANI
[2023-03-17 10:10:42,565] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:10:42,566] [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_002389295.1	s__UBA8752 sp002389295	99.3562	660	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.36	99.34	0.83	0.82	3	conclusive
GCA_016780385.1	s__UBA8752 sp016780385	79.0472	290	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172485.2	s__UBA8752 sp002172485	78.7675	203	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862785.1	s__UBA8752 sp002862785	78.5078	303	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683735.1	s__UBA8752 sp002683735	78.3056	166	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336475.1	s__UBA8752 sp002336475	78.2762	304	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.51	99.51	0.88	0.88	2	-
GCA_905478795.1	s__UBA8752 sp905478795	78.2639	320	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522855.1	s__UBA8752 sp011522855	77.6001	233	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535565.1	s__UBA8752 sp902535565	77.5176	90	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729115.1	s__UBA11663 sp002729115	76.4669	61	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	-
GCA_002863145.1	s__UBA11663 sp002863145	76.0601	57	806	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
--------------------------------------------------------------------------------
[2023-03-17 10:10:42,580] [INFO] GTDB search result was written to OceanDNA-b12001/result_gtdb.tsv
[2023-03-17 10:10:42,581] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:10:42,582] [INFO] DFAST_QC result json was written to OceanDNA-b12001/dqc_result.json
[2023-03-17 10:10:42,582] [INFO] DFAST_QC completed!
[2023-03-17 10:10:42,582] [INFO] Total running time: 0h2m3s