[2023-03-16 05:41:22,600] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:41:22,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:41:22,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference
[2023-03-16 05:41:23,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:41:23,675] [INFO] Task started: Prodigal
[2023-03-16 05:41:23,675] [INFO] Running command: cat /var/lib/cwl/stg3b46a267-eb08-42f9-9626-b6bb00fa0c8c/OceanDNA-b3473.fa | prodigal -d OceanDNA-b3473/cds.fna -a OceanDNA-b3473/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:41:47,541] [INFO] Task succeeded: Prodigal
[2023-03-16 05:41:47,542] [INFO] Task started: HMMsearch
[2023-03-16 05:41:47,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b3473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference/reference_markers.hmm OceanDNA-b3473/protein.faa > /dev/null
[2023-03-16 05:41:47,751] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:41:47,751] [INFO] Found 6/6 markers.
[2023-03-16 05:41:47,775] [INFO] Query marker FASTA was written to OceanDNA-b3473/markers.fasta
[2023-03-16 05:41:47,775] [INFO] Task started: Blastn
[2023-03-16 05:41:47,775] [INFO] Running command: blastn -query OceanDNA-b3473/markers.fasta -db /var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference/reference_markers.fasta -out OceanDNA-b3473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:41:48,301] [INFO] Task succeeded: Blastn
[2023-03-16 05:41:48,301] [INFO] Selected 29 target genomes.
[2023-03-16 05:41:48,302] [INFO] Target genome list was writen to OceanDNA-b3473/target_genomes.txt
[2023-03-16 05:41:48,316] [INFO] Task started: fastANI
[2023-03-16 05:41:48,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b46a267-eb08-42f9-9626-b6bb00fa0c8c/OceanDNA-b3473.fa --refList OceanDNA-b3473/target_genomes.txt --output OceanDNA-b3473/fastani_result.tsv --threads 1
[2023-03-16 05:42:06,523] [INFO] Task succeeded: fastANI
[2023-03-16 05:42:06,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:42:06,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:42:06,524] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:42:06,524] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:42:06,524] [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
--------------------------------------------------------------------------------
[2023-03-16 05:42:06,525] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3473/tc_result.tsv
[2023-03-16 05:42:06,525] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:42:06,525] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:42:06,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference/checkm_data
[2023-03-16 05:42:06,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:42:06,683] [INFO] Task started: CheckM
[2023-03-16 05:42:06,683] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3473/checkm_input OceanDNA-b3473/checkm_result
[2023-03-16 05:43:06,641] [INFO] Task succeeded: CheckM
[2023-03-16 05:43:06,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.42%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:43:06,644] [INFO] ===== Completeness check finished =====
[2023-03-16 05:43:06,644] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:43:06,644] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3473/markers.fasta)
[2023-03-16 05:43:06,646] [INFO] Task started: Blastn
[2023-03-16 05:43:06,646] [INFO] Running command: blastn -query OceanDNA-b3473/markers.fasta -db /var/lib/cwl/stgbf5d2de4-1c48-4f7a-84ff-cde2c1a8ade3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:43:07,362] [INFO] Task succeeded: Blastn
[2023-03-16 05:43:07,363] [INFO] Selected 19 target genomes.
[2023-03-16 05:43:07,363] [INFO] Target genome list was writen to OceanDNA-b3473/target_genomes_gtdb.txt
[2023-03-16 05:43:07,379] [INFO] Task started: fastANI
[2023-03-16 05:43:07,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b46a267-eb08-42f9-9626-b6bb00fa0c8c/OceanDNA-b3473.fa --refList OceanDNA-b3473/target_genomes_gtdb.txt --output OceanDNA-b3473/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:43:19,584] [INFO] Task succeeded: fastANI
[2023-03-16 05:43:19,589] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:43:19,589] [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_013203805.1	s__GCA-002708315 sp013203805	91.8198	865	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845105.1	s__GCA-002708315 sp016845105	78.1295	456	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382445.1	s__GCA-002708315 sp014382445	78.0411	252	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.88	99.88	0.96	0.96	2	-
GCA_018661505.1	s__GCA-002708315 sp018661505	76.6355	92	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	99.95	99.92	0.97	0.96	16	-
GCA_002686705.1	s__GCA-002708315 sp002686705	76.4887	150	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__GCA-002708315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002771745.1	s__UBA6244 sp002771745	75.9988	51	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6244	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869365.1	s__BM524 sp002869365	75.7356	80	1191	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__BM524	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:43:19,589] [INFO] GTDB search result was written to OceanDNA-b3473/result_gtdb.tsv
[2023-03-16 05:43:19,589] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:43:19,590] [INFO] DFAST_QC result json was written to OceanDNA-b3473/dqc_result.json
[2023-03-16 05:43:19,590] [INFO] DFAST_QC completed!
[2023-03-16 05:43:19,590] [INFO] Total running time: 0h1m57s