[2023-03-17 09:51:05,581] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:51:05,581] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:51:05,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference
[2023-03-17 09:51:06,735] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:51:06,735] [INFO] Task started: Prodigal
[2023-03-17 09:51:06,736] [INFO] Running command: cat /var/lib/cwl/stg380633b5-2967-4742-be4f-78ef94c73171/OceanDNA-b5270.fa | prodigal -d OceanDNA-b5270/cds.fna -a OceanDNA-b5270/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:51:19,684] [INFO] Task succeeded: Prodigal
[2023-03-17 09:51:19,684] [INFO] Task started: HMMsearch
[2023-03-17 09:51:19,684] [INFO] Running command: hmmsearch --tblout OceanDNA-b5270/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference/reference_markers.hmm OceanDNA-b5270/protein.faa > /dev/null
[2023-03-17 09:51:19,861] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:51:19,862] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg380633b5-2967-4742-be4f-78ef94c73171/OceanDNA-b5270.fa]
[2023-03-17 09:51:19,878] [INFO] Query marker FASTA was written to OceanDNA-b5270/markers.fasta
[2023-03-17 09:51:19,879] [INFO] Task started: Blastn
[2023-03-17 09:51:19,879] [INFO] Running command: blastn -query OceanDNA-b5270/markers.fasta -db /var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference/reference_markers.fasta -out OceanDNA-b5270/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:51:20,450] [INFO] Task succeeded: Blastn
[2023-03-17 09:51:20,451] [INFO] Selected 25 target genomes.
[2023-03-17 09:51:20,451] [INFO] Target genome list was writen to OceanDNA-b5270/target_genomes.txt
[2023-03-17 09:51:20,466] [INFO] Task started: fastANI
[2023-03-17 09:51:20,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg380633b5-2967-4742-be4f-78ef94c73171/OceanDNA-b5270.fa --refList OceanDNA-b5270/target_genomes.txt --output OceanDNA-b5270/fastani_result.tsv --threads 1
[2023-03-17 09:51:34,986] [INFO] Task succeeded: fastANI
[2023-03-17 09:51:34,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:51:34,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:51:34,990] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:51:34,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:51:34,990] [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
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.5318	55	524	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:51:34,990] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5270/tc_result.tsv
[2023-03-17 09:51:34,990] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:51:34,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:51:34,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference/checkm_data
[2023-03-17 09:51:34,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:51:34,995] [INFO] Task started: CheckM
[2023-03-17 09:51:34,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5270/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5270/checkm_input OceanDNA-b5270/checkm_result
[2023-03-17 09:52:13,285] [INFO] Task succeeded: CheckM
[2023-03-17 09:52:13,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.93%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:52:13,288] [INFO] ===== Completeness check finished =====
[2023-03-17 09:52:13,288] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:52:13,288] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5270/markers.fasta)
[2023-03-17 09:52:13,289] [INFO] Task started: Blastn
[2023-03-17 09:52:13,289] [INFO] Running command: blastn -query OceanDNA-b5270/markers.fasta -db /var/lib/cwl/stg3ebd5bc6-bd8d-4ce6-b35a-fccd8581ed65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5270/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:52:14,203] [INFO] Task succeeded: Blastn
[2023-03-17 09:52:14,205] [INFO] Selected 27 target genomes.
[2023-03-17 09:52:14,205] [INFO] Target genome list was writen to OceanDNA-b5270/target_genomes_gtdb.txt
[2023-03-17 09:52:14,937] [INFO] Task started: fastANI
[2023-03-17 09:52:14,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg380633b5-2967-4742-be4f-78ef94c73171/OceanDNA-b5270.fa --refList OceanDNA-b5270/target_genomes_gtdb.txt --output OceanDNA-b5270/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:52:28,386] [INFO] Task succeeded: fastANI
[2023-03-17 09:52:28,392] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:52:28,392] [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_903945495.1	s__M0103 sp903945495	78.2136	192	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_017984635.1	s__M0103 sp017984635	77.617	97	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930085.1	s__M0103 sp903930085	77.38	64	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983465.1	s__UBA952 sp017983465	77.0729	52	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.99	99.99	0.99	0.99	2	-
GCA_009885545.1	s__M0103 sp009885545	76.9185	120	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	76.6136	50	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	76.5839	75	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.5318	55	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733985.1	s__UBA4466 sp002733985	76.4379	51	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:52:28,392] [INFO] GTDB search result was written to OceanDNA-b5270/result_gtdb.tsv
[2023-03-17 09:52:28,393] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:52:28,394] [INFO] DFAST_QC result json was written to OceanDNA-b5270/dqc_result.json
[2023-03-17 09:52:28,394] [INFO] DFAST_QC completed!
[2023-03-17 09:52:28,394] [INFO] Total running time: 0h1m23s