[2023-03-17 00:17:04,517] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference
[2023-03-17 00:17:05,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,623] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,623] [INFO] Running command: cat /var/lib/cwl/stgd2c5c3c0-83ac-4995-b113-b01109b64742/OceanDNA-b34567.fa | prodigal -d OceanDNA-b34567/cds.fna -a OceanDNA-b34567/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:33,075] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:33,075] [INFO] Task started: HMMsearch
[2023-03-17 00:17:33,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b34567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference/reference_markers.hmm OceanDNA-b34567/protein.faa > /dev/null
[2023-03-17 00:17:33,323] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:33,324] [INFO] Found 6/6 markers.
[2023-03-17 00:17:33,351] [INFO] Query marker FASTA was written to OceanDNA-b34567/markers.fasta
[2023-03-17 00:17:33,353] [INFO] Task started: Blastn
[2023-03-17 00:17:33,353] [INFO] Running command: blastn -query OceanDNA-b34567/markers.fasta -db /var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference/reference_markers.fasta -out OceanDNA-b34567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:33,986] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:33,987] [INFO] Selected 16 target genomes.
[2023-03-17 00:17:33,987] [INFO] Target genome list was writen to OceanDNA-b34567/target_genomes.txt
[2023-03-17 00:17:33,995] [INFO] Task started: fastANI
[2023-03-17 00:17:33,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c5c3c0-83ac-4995-b113-b01109b64742/OceanDNA-b34567.fa --refList OceanDNA-b34567/target_genomes.txt --output OceanDNA-b34567/fastani_result.tsv --threads 1
[2023-03-17 00:17:47,092] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:47,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:47,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:47,101] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:47,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:17:47,101] [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
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	90.344	1261	1607	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	89.7723	1204	1607	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	80.9579	734	1607	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	80.884	747	1607	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	78.1443	120	1607	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	77.6723	129	1607	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.5978	165	1607	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	77.5444	138	1607	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.5299	209	1607	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	77.362	129	1607	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.2206	160	1607	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:17:47,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34567/tc_result.tsv
[2023-03-17 00:17:47,101] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:47,101] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:47,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference/checkm_data
[2023-03-17 00:17:47,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:47,116] [INFO] Task started: CheckM
[2023-03-17 00:17:47,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34567/checkm_input OceanDNA-b34567/checkm_result
[2023-03-17 00:18:54,565] [INFO] Task succeeded: CheckM
[2023-03-17 00:18:54,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.45%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:18:54,635] [INFO] ===== Completeness check finished =====
[2023-03-17 00:18:54,636] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:18:54,636] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34567/markers.fasta)
[2023-03-17 00:18:54,637] [INFO] Task started: Blastn
[2023-03-17 00:18:54,637] [INFO] Running command: blastn -query OceanDNA-b34567/markers.fasta -db /var/lib/cwl/stgdda0259c-db08-43ee-82ef-a3ef8c93938b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:18:55,515] [INFO] Task succeeded: Blastn
[2023-03-17 00:18:55,516] [INFO] Selected 7 target genomes.
[2023-03-17 00:18:55,516] [INFO] Target genome list was writen to OceanDNA-b34567/target_genomes_gtdb.txt
[2023-03-17 00:18:55,521] [INFO] Task started: fastANI
[2023-03-17 00:18:55,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c5c3c0-83ac-4995-b113-b01109b64742/OceanDNA-b34567.fa --refList OceanDNA-b34567/target_genomes_gtdb.txt --output OceanDNA-b34567/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:19:02,620] [INFO] Task succeeded: fastANI
[2023-03-17 00:19:02,625] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:19:02,625] [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_018222405.1	s__Alteromonas sp018222405	90.6296	1278	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	90.344	1261	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	90.1773	1109	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_002993365.1	s__Alteromonas alba	89.7803	1203	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	89.6166	1004	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_001758465.1	s__Alteromonas lipolytica	80.9565	735	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003584565.2	s__Alteromonas sp002729795	77.7648	198	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:19:02,626] [INFO] GTDB search result was written to OceanDNA-b34567/result_gtdb.tsv
[2023-03-17 00:19:02,626] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:19:02,627] [INFO] DFAST_QC result json was written to OceanDNA-b34567/dqc_result.json
[2023-03-17 00:19:02,627] [INFO] DFAST_QC completed!
[2023-03-17 00:19:02,627] [INFO] Total running time: 0h1m58s