[2023-03-16 09:43:37,171] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,171] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,171] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference
[2023-03-16 09:43:39,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,239] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,239] [INFO] Running command: cat /var/lib/cwl/stg8004db72-297e-4842-8f39-5356a2d7ee09/OceanDNA-b13057.fa | prodigal -d OceanDNA-b13057/cds.fna -a OceanDNA-b13057/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:44:07,151] [INFO] Task succeeded: Prodigal
[2023-03-16 09:44:07,151] [INFO] Task started: HMMsearch
[2023-03-16 09:44:07,151] [INFO] Running command: hmmsearch --tblout OceanDNA-b13057/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference/reference_markers.hmm OceanDNA-b13057/protein.faa > /dev/null
[2023-03-16 09:44:07,354] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:44:07,355] [INFO] Found 6/6 markers.
[2023-03-16 09:44:07,378] [INFO] Query marker FASTA was written to OceanDNA-b13057/markers.fasta
[2023-03-16 09:44:07,378] [INFO] Task started: Blastn
[2023-03-16 09:44:07,378] [INFO] Running command: blastn -query OceanDNA-b13057/markers.fasta -db /var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference/reference_markers.fasta -out OceanDNA-b13057/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:07,893] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:07,894] [INFO] Selected 19 target genomes.
[2023-03-16 09:44:07,894] [INFO] Target genome list was writen to OceanDNA-b13057/target_genomes.txt
[2023-03-16 09:44:08,103] [INFO] Task started: fastANI
[2023-03-16 09:44:08,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg8004db72-297e-4842-8f39-5356a2d7ee09/OceanDNA-b13057.fa --refList OceanDNA-b13057/target_genomes.txt --output OceanDNA-b13057/fastani_result.tsv --threads 1
[2023-03-16 09:44:19,383] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:19,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:44:19,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:44:19,388] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:44:19,388] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:44:19,388] [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
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	79.9533	97	1289	95	below_threshold
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	79.1385	100	1289	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	76.6704	55	1289	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:44:19,388] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13057/tc_result.tsv
[2023-03-16 09:44:19,388] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:44:19,388] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:44:19,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference/checkm_data
[2023-03-16 09:44:19,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:44:19,394] [INFO] Task started: CheckM
[2023-03-16 09:44:19,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13057/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13057/checkm_input OceanDNA-b13057/checkm_result
[2023-03-16 09:45:29,864] [INFO] Task succeeded: CheckM
[2023-03-16 09:45:29,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:45:29,926] [INFO] ===== Completeness check finished =====
[2023-03-16 09:45:29,927] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:45:29,927] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13057/markers.fasta)
[2023-03-16 09:45:29,927] [INFO] Task started: Blastn
[2023-03-16 09:45:29,927] [INFO] Running command: blastn -query OceanDNA-b13057/markers.fasta -db /var/lib/cwl/stgd3881e39-9a63-43c0-a53c-c4583b3ff0ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13057/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:45:30,678] [INFO] Task succeeded: Blastn
[2023-03-16 09:45:30,686] [INFO] Selected 20 target genomes.
[2023-03-16 09:45:30,687] [INFO] Target genome list was writen to OceanDNA-b13057/target_genomes_gtdb.txt
[2023-03-16 09:45:30,758] [INFO] Task started: fastANI
[2023-03-16 09:45:30,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg8004db72-297e-4842-8f39-5356a2d7ee09/OceanDNA-b13057.fa --refList OceanDNA-b13057/target_genomes_gtdb.txt --output OceanDNA-b13057/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:45:42,941] [INFO] Task succeeded: fastANI
[2023-03-16 09:45:42,949] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:45:42,949] [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_002480645.1	s__UBA7797 sp002480645	99.9696	1255	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA7797	95.0	99.98	99.91	0.99	0.98	7	conclusive
GCA_002694685.1	s__Gracilimonas sp002694685	82.358	100	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_017641085.1	s__Gracilimonas sp017641085	80.529	112	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002911695.1	s__Gracilimonas amylolytica	79.9533	97	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762685.1	s__Gracilimonas sp014762685	79.9503	81	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696035.1	s__Gracilimonas sp002696035	77.6352	89	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017640665.1	s__RHLJ01 sp017640665	77.0667	129	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017640605.1	s__HXMU1420-13 sp017640605	76.9953	102	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795005.1	s__RHLJ01 sp017795005	76.7025	129	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643365.1	s__HXMU1420-13 sp017643365	76.6672	126	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711805.1	s__MES10 sp009711805	76.5052	53	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__MES10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640785.1	s__Balneola sp017640785	76.3235	87	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650905.1	s__Balneola sp001650905	76.0957	97	1289	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:45:42,949] [INFO] GTDB search result was written to OceanDNA-b13057/result_gtdb.tsv
[2023-03-16 09:45:42,949] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:45:42,950] [INFO] DFAST_QC result json was written to OceanDNA-b13057/dqc_result.json
[2023-03-16 09:45:42,950] [INFO] DFAST_QC completed!
[2023-03-16 09:45:42,950] [INFO] Total running time: 0h2m6s