[2023-03-15 23:42:29,663] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,664] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference
[2023-03-15 23:42:31,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,275] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,276] [INFO] Running command: cat /var/lib/cwl/stg1a71251d-f98a-45e6-9be0-8e38dec438e5/OceanDNA-b11968.fa | prodigal -d OceanDNA-b11968/cds.fna -a OceanDNA-b11968/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:52,337] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:52,337] [INFO] Task started: HMMsearch
[2023-03-15 23:42:52,337] [INFO] Running command: hmmsearch --tblout OceanDNA-b11968/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference/reference_markers.hmm OceanDNA-b11968/protein.faa > /dev/null
[2023-03-15 23:42:52,498] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:52,498] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a71251d-f98a-45e6-9be0-8e38dec438e5/OceanDNA-b11968.fa]
[2023-03-15 23:42:52,514] [INFO] Query marker FASTA was written to OceanDNA-b11968/markers.fasta
[2023-03-15 23:42:52,514] [INFO] Task started: Blastn
[2023-03-15 23:42:52,514] [INFO] Running command: blastn -query OceanDNA-b11968/markers.fasta -db /var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference/reference_markers.fasta -out OceanDNA-b11968/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:53,051] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:53,052] [INFO] Selected 25 target genomes.
[2023-03-15 23:42:53,053] [INFO] Target genome list was writen to OceanDNA-b11968/target_genomes.txt
[2023-03-15 23:42:53,070] [INFO] Task started: fastANI
[2023-03-15 23:42:53,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a71251d-f98a-45e6-9be0-8e38dec438e5/OceanDNA-b11968.fa --refList OceanDNA-b11968/target_genomes.txt --output OceanDNA-b11968/fastani_result.tsv --threads 1
[2023-03-15 23:43:10,162] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:10,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:43:10,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:43:10,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:43:10,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:43:10,163] [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
--------------------------------------------------------------------------------
[2023-03-15 23:43:10,163] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11968/tc_result.tsv
[2023-03-15 23:43:10,163] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:43:10,163] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:43:10,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference/checkm_data
[2023-03-15 23:43:10,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:43:10,285] [INFO] Task started: CheckM
[2023-03-15 23:43:10,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11968/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11968/checkm_input OceanDNA-b11968/checkm_result
[2023-03-15 23:44:09,925] [INFO] Task succeeded: CheckM
[2023-03-15 23:44:09,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:44:09,927] [INFO] ===== Completeness check finished =====
[2023-03-15 23:44:09,927] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:44:09,928] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11968/markers.fasta)
[2023-03-15 23:44:09,929] [INFO] Task started: Blastn
[2023-03-15 23:44:09,929] [INFO] Running command: blastn -query OceanDNA-b11968/markers.fasta -db /var/lib/cwl/stg425e07fc-427e-4d05-9832-3750bc6e1c0b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11968/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:44:10,722] [INFO] Task succeeded: Blastn
[2023-03-15 23:44:10,723] [INFO] Selected 17 target genomes.
[2023-03-15 23:44:10,723] [INFO] Target genome list was writen to OceanDNA-b11968/target_genomes_gtdb.txt
[2023-03-15 23:44:10,742] [INFO] Task started: fastANI
[2023-03-15 23:44:10,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a71251d-f98a-45e6-9be0-8e38dec438e5/OceanDNA-b11968.fa --refList OceanDNA-b11968/target_genomes_gtdb.txt --output OceanDNA-b11968/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:44:19,163] [INFO] Task succeeded: fastANI
[2023-03-15 23:44:19,169] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:44:19,170] [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_011522855.1	s__UBA8752 sp011522855	82.7855	345	639	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	82.7356	419	639	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	80.3669	244	639	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	79.7711	203	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389295.1	s__UBA8752 sp002389295	78.1412	227	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.36	99.34	0.83	0.82	3	-
GCA_016780385.1	s__UBA8752 sp016780385	77.9761	196	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478795.1	s__UBA8752 sp905478795	77.2256	186	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720375.1	s__UBA8752 sp002720375	77.1304	98	639	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	77.0157	156	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA8752	95.0	99.51	99.51	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 23:44:19,170] [INFO] GTDB search result was written to OceanDNA-b11968/result_gtdb.tsv
[2023-03-15 23:44:19,171] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:44:19,173] [INFO] DFAST_QC result json was written to OceanDNA-b11968/dqc_result.json
[2023-03-15 23:44:19,173] [INFO] DFAST_QC completed!
[2023-03-15 23:44:19,173] [INFO] Total running time: 0h1m50s