[2023-03-15 11:09:10,792] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,792] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference
[2023-03-15 11:09:11,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:11,937] [INFO] Task started: Prodigal
[2023-03-15 11:09:11,937] [INFO] Running command: cat /var/lib/cwl/stg89b6435c-dd6a-43cf-bdcf-21ea9cab2e40/OceanDNA-b12887.fa | prodigal -d OceanDNA-b12887/cds.fna -a OceanDNA-b12887/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:30,872] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:30,872] [INFO] Task started: HMMsearch
[2023-03-15 11:09:30,872] [INFO] Running command: hmmsearch --tblout OceanDNA-b12887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference/reference_markers.hmm OceanDNA-b12887/protein.faa > /dev/null
[2023-03-15 11:09:31,167] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:31,168] [INFO] Found 6/6 markers.
[2023-03-15 11:09:31,193] [INFO] Query marker FASTA was written to OceanDNA-b12887/markers.fasta
[2023-03-15 11:09:31,193] [INFO] Task started: Blastn
[2023-03-15 11:09:31,193] [INFO] Running command: blastn -query OceanDNA-b12887/markers.fasta -db /var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference/reference_markers.fasta -out OceanDNA-b12887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:31,813] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:31,814] [INFO] Selected 24 target genomes.
[2023-03-15 11:09:31,814] [INFO] Target genome list was writen to OceanDNA-b12887/target_genomes.txt
[2023-03-15 11:09:31,827] [INFO] Task started: fastANI
[2023-03-15 11:09:31,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b6435c-dd6a-43cf-bdcf-21ea9cab2e40/OceanDNA-b12887.fa --refList OceanDNA-b12887/target_genomes.txt --output OceanDNA-b12887/fastani_result.tsv --threads 1
[2023-03-15 11:09:46,389] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:46,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:46,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:46,392] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:46,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:46,392] [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
Ignavibacterium album	strain=JCM 16511	GCA_000258405.1	591197	591197	type	True	75.761	67	1227	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:46,393] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12887/tc_result.tsv
[2023-03-15 11:09:46,393] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:46,393] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:46,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference/checkm_data
[2023-03-15 11:09:46,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:46,400] [INFO] Task started: CheckM
[2023-03-15 11:09:46,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12887/checkm_input OceanDNA-b12887/checkm_result
[2023-03-15 11:10:34,836] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:34,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:34,839] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:34,840] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:34,840] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12887/markers.fasta)
[2023-03-15 11:10:34,840] [INFO] Task started: Blastn
[2023-03-15 11:10:34,840] [INFO] Running command: blastn -query OceanDNA-b12887/markers.fasta -db /var/lib/cwl/stg356b04ab-7758-4eba-b0e1-4033b45695ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:35,712] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:35,713] [INFO] Selected 20 target genomes.
[2023-03-15 11:10:35,713] [INFO] Target genome list was writen to OceanDNA-b12887/target_genomes_gtdb.txt
[2023-03-15 11:10:35,732] [INFO] Task started: fastANI
[2023-03-15 11:10:35,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b6435c-dd6a-43cf-bdcf-21ea9cab2e40/OceanDNA-b12887.fa --refList OceanDNA-b12887/target_genomes_gtdb.txt --output OceanDNA-b12887/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:46,911] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:46,919] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:46,919] [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_002698995.1	s__GCA-2698995 sp002698995	80.7104	694	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2698995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829205.1	s__JAHJUE01 sp018829205	77.4378	138	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__JAHJUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599395.1	s__SURF-28 sp003599395	76.392	81	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__SURF-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112585.1	s__IGN16 sp013112585	76.2434	98	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__IGN16	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016708125.1	s__GCA-2746605 sp016708125	76.1477	170	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011049495.1	s__SURF-28 sp011049495	76.1277	88	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__SURF-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280825.1	s__Fen-1258 sp007280825	76.126	52	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__Fen-1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011368355.1	s__Ignavibacterium album_A	75.8711	62	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__Ignavibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707585.1	s__IGN3 sp016707585	75.7735	81	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Ignavibacteriaceae;g__IGN3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713565.1	s__GCA-2746605 sp016713565	75.7156	118	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	99.17	99.17	0.95	0.95	2	-
GCA_002839805.1	s__PGYT01 sp002839805	75.7053	73	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__PGYT01	95.0	98.73	98.73	0.98	0.98	2	-
GCA_002790395.1	s__UM-FILTER-34-10 sp002790395	75.5683	63	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__UM-FILTER-34-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599415.1	s__SURF-24 sp003599415	75.483	60	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__SURF-24;g__SURF-24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773205.1	s__XYB12-FULL-38-5 sp009773205	75.4019	80	1227	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__XYB12-FULL-38-5	95.0	99.94	99.94	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:46,920] [INFO] GTDB search result was written to OceanDNA-b12887/result_gtdb.tsv
[2023-03-15 11:10:46,920] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:46,921] [INFO] DFAST_QC result json was written to OceanDNA-b12887/dqc_result.json
[2023-03-15 11:10:46,921] [INFO] DFAST_QC completed!
[2023-03-15 11:10:46,921] [INFO] Total running time: 0h1m36s