[2023-03-17 23:49:09,982] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:49:09,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:49:09,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference
[2023-03-17 23:49:11,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:49:11,101] [INFO] Task started: Prodigal
[2023-03-17 23:49:11,101] [INFO] Running command: cat /var/lib/cwl/stg110331ab-7de0-46cc-9546-4dd386a4d877/OceanDNA-b15453.fa | prodigal -d OceanDNA-b15453/cds.fna -a OceanDNA-b15453/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:49:32,495] [INFO] Task succeeded: Prodigal
[2023-03-17 23:49:32,496] [INFO] Task started: HMMsearch
[2023-03-17 23:49:32,496] [INFO] Running command: hmmsearch --tblout OceanDNA-b15453/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference/reference_markers.hmm OceanDNA-b15453/protein.faa > /dev/null
[2023-03-17 23:49:32,670] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:49:32,670] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg110331ab-7de0-46cc-9546-4dd386a4d877/OceanDNA-b15453.fa]
[2023-03-17 23:49:32,692] [INFO] Query marker FASTA was written to OceanDNA-b15453/markers.fasta
[2023-03-17 23:49:32,692] [INFO] Task started: Blastn
[2023-03-17 23:49:32,692] [INFO] Running command: blastn -query OceanDNA-b15453/markers.fasta -db /var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference/reference_markers.fasta -out OceanDNA-b15453/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:33,184] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:33,185] [INFO] Selected 15 target genomes.
[2023-03-17 23:49:33,185] [INFO] Target genome list was writen to OceanDNA-b15453/target_genomes.txt
[2023-03-17 23:49:33,196] [INFO] Task started: fastANI
[2023-03-17 23:49:33,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg110331ab-7de0-46cc-9546-4dd386a4d877/OceanDNA-b15453.fa --refList OceanDNA-b15453/target_genomes.txt --output OceanDNA-b15453/fastani_result.tsv --threads 1
[2023-03-17 23:49:48,264] [INFO] Task succeeded: fastANI
[2023-03-17 23:49:48,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:49:48,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:49:48,265] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:49:48,265] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:49:48,265] [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 23:49:48,271] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15453/tc_result.tsv
[2023-03-17 23:49:48,278] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:49:48,278] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:49:48,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference/checkm_data
[2023-03-17 23:49:48,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:49:48,285] [INFO] Task started: CheckM
[2023-03-17 23:49:48,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15453/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15453/checkm_input OceanDNA-b15453/checkm_result
[2023-03-17 23:50:41,522] [INFO] Task succeeded: CheckM
[2023-03-17 23:50:41,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:50:41,535] [INFO] ===== Completeness check finished =====
[2023-03-17 23:50:41,536] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:50:41,536] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15453/markers.fasta)
[2023-03-17 23:50:41,537] [INFO] Task started: Blastn
[2023-03-17 23:50:41,537] [INFO] Running command: blastn -query OceanDNA-b15453/markers.fasta -db /var/lib/cwl/stg9af0bd35-f729-4564-bbf7-79fa1b06e01e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15453/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:50:42,198] [INFO] Task succeeded: Blastn
[2023-03-17 23:50:42,198] [INFO] Selected 18 target genomes.
[2023-03-17 23:50:42,199] [INFO] Target genome list was writen to OceanDNA-b15453/target_genomes_gtdb.txt
[2023-03-17 23:50:42,213] [INFO] Task started: fastANI
[2023-03-17 23:50:42,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg110331ab-7de0-46cc-9546-4dd386a4d877/OceanDNA-b15453.fa --refList OceanDNA-b15453/target_genomes_gtdb.txt --output OceanDNA-b15453/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:50:50,367] [INFO] Task succeeded: fastANI
[2023-03-17 23:50:50,374] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:50:50,374] [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_002710215.1	s__UBA11650 sp002710215	76.6943	150	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	99.22	99.06	0.76	0.73	3	-
GCA_002721995.1	s__UBA9611 sp002721995	76.5896	128	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002698265.1	s__UBA9611 sp002698265	76.3831	65	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.74	98.13	0.78	0.72	6	-
GCA_002816575.1	s__UBA9611 sp002816575	76.3497	100	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392075.1	s__UBA9611 sp009392075	76.3103	62	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_013204585.1	s__UBA9611 sp013204585	76.1844	65	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840175.1	s__VXOI01 sp009840175	76.0498	111	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
GCA_002746355.1	s__UBA9611 sp002746355	75.9703	138	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_016872385.1	s__SHYG01 sp016872385	75.9238	98	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708395.1	s__UBA11650 sp002708395	75.8348	74	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.39	98.39	0.67	0.67	2	-
GCA_002328185.1	s__UBA9611 sp002328185	75.7873	125	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.06	0.94	0.90	6	-
GCA_002730485.1	s__UBA9611 sp002730485	75.6185	52	1143	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:50:50,378] [INFO] GTDB search result was written to OceanDNA-b15453/result_gtdb.tsv
[2023-03-17 23:50:50,379] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:50:50,380] [INFO] DFAST_QC result json was written to OceanDNA-b15453/dqc_result.json
[2023-03-17 23:50:50,380] [INFO] DFAST_QC completed!
[2023-03-17 23:50:50,380] [INFO] Total running time: 0h1m40s