[2023-03-19 04:29:37,771] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,772] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference
[2023-03-19 04:29:38,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stg9c8e340b-4754-4cb5-beb7-2fb9d96682bf/OceanDNA-b5277.fa | prodigal -d OceanDNA-b5277/cds.fna -a OceanDNA-b5277/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:59,967] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:59,968] [INFO] Task started: HMMsearch
[2023-03-19 04:29:59,968] [INFO] Running command: hmmsearch --tblout OceanDNA-b5277/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference/reference_markers.hmm OceanDNA-b5277/protein.faa > /dev/null
[2023-03-19 04:30:00,154] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:00,155] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9c8e340b-4754-4cb5-beb7-2fb9d96682bf/OceanDNA-b5277.fa]
[2023-03-19 04:30:00,175] [INFO] Query marker FASTA was written to OceanDNA-b5277/markers.fasta
[2023-03-19 04:30:00,175] [INFO] Task started: Blastn
[2023-03-19 04:30:00,175] [INFO] Running command: blastn -query OceanDNA-b5277/markers.fasta -db /var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference/reference_markers.fasta -out OceanDNA-b5277/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:00,695] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:00,695] [INFO] Selected 17 target genomes.
[2023-03-19 04:30:00,696] [INFO] Target genome list was writen to OceanDNA-b5277/target_genomes.txt
[2023-03-19 04:30:00,703] [INFO] Task started: fastANI
[2023-03-19 04:30:00,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c8e340b-4754-4cb5-beb7-2fb9d96682bf/OceanDNA-b5277.fa --refList OceanDNA-b5277/target_genomes.txt --output OceanDNA-b5277/fastani_result.tsv --threads 1
[2023-03-19 04:30:10,725] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:10,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:10,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:10,729] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:10,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:10,730] [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
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	77.1379	148	1020	95	below_threshold
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	77.0582	166	1020	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	76.5047	69	1020	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:10,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5277/tc_result.tsv
[2023-03-19 04:30:10,730] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:10,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:10,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference/checkm_data
[2023-03-19 04:30:10,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:10,735] [INFO] Task started: CheckM
[2023-03-19 04:30:10,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5277/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5277/checkm_input OceanDNA-b5277/checkm_result
[2023-03-19 04:31:05,536] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:05,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:05,538] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:05,538] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:05,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5277/markers.fasta)
[2023-03-19 04:31:05,540] [INFO] Task started: Blastn
[2023-03-19 04:31:05,540] [INFO] Running command: blastn -query OceanDNA-b5277/markers.fasta -db /var/lib/cwl/stg8f5667f9-2d36-451f-9d6f-7e4474435718/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5277/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:06,227] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:06,228] [INFO] Selected 14 target genomes.
[2023-03-19 04:31:06,228] [INFO] Target genome list was writen to OceanDNA-b5277/target_genomes_gtdb.txt
[2023-03-19 04:31:06,292] [INFO] Task started: fastANI
[2023-03-19 04:31:06,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c8e340b-4754-4cb5-beb7-2fb9d96682bf/OceanDNA-b5277.fa --refList OceanDNA-b5277/target_genomes_gtdb.txt --output OceanDNA-b5277/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:14,435] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:14,440] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:31:14,440] [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_905478225.1	s__Crocinitomix sp905478225	98.0998	940	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013138735.1	s__Crocinitomix sp013138735	79.8766	660	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621625.1	s__Crocinitomix catalasitica	77.1379	148	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661595.2	s__Crocinitomix algicola	77.0582	166	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	76.5343	68	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662905.1	s__Putridiphycobacter sp015662905	75.9704	50	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709005.1	s__JADJGJ01 sp016709005	75.8261	60	1020	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	98.05	97.64	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:14,441] [INFO] GTDB search result was written to OceanDNA-b5277/result_gtdb.tsv
[2023-03-19 04:31:14,441] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:14,442] [INFO] DFAST_QC result json was written to OceanDNA-b5277/dqc_result.json
[2023-03-19 04:31:14,442] [INFO] DFAST_QC completed!
[2023-03-19 04:31:14,442] [INFO] Total running time: 0h1m37s