[2023-03-16 09:47:30,750] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:47:30,751] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:47:30,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference
[2023-03-16 09:47:31,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:47:31,887] [INFO] Task started: Prodigal
[2023-03-16 09:47:31,887] [INFO] Running command: cat /var/lib/cwl/stg574426a4-79e7-4d3a-b523-528121406f61/OceanDNA-b12971.fa | prodigal -d OceanDNA-b12971/cds.fna -a OceanDNA-b12971/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:47:57,638] [INFO] Task succeeded: Prodigal
[2023-03-16 09:47:57,639] [INFO] Task started: HMMsearch
[2023-03-16 09:47:57,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b12971/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference/reference_markers.hmm OceanDNA-b12971/protein.faa > /dev/null
[2023-03-16 09:47:57,835] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:47:57,835] [INFO] Found 6/6 markers.
[2023-03-16 09:47:57,860] [INFO] Query marker FASTA was written to OceanDNA-b12971/markers.fasta
[2023-03-16 09:47:57,861] [INFO] Task started: Blastn
[2023-03-16 09:47:57,862] [INFO] Running command: blastn -query OceanDNA-b12971/markers.fasta -db /var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference/reference_markers.fasta -out OceanDNA-b12971/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:47:58,389] [INFO] Task succeeded: Blastn
[2023-03-16 09:47:58,391] [INFO] Selected 20 target genomes.
[2023-03-16 09:47:58,392] [INFO] Target genome list was writen to OceanDNA-b12971/target_genomes.txt
[2023-03-16 09:47:58,541] [INFO] Task started: fastANI
[2023-03-16 09:47:58,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg574426a4-79e7-4d3a-b523-528121406f61/OceanDNA-b12971.fa --refList OceanDNA-b12971/target_genomes.txt --output OceanDNA-b12971/fastani_result.tsv --threads 1
[2023-03-16 09:48:10,714] [INFO] Task succeeded: fastANI
[2023-03-16 09:48:10,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:48:10,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:48:10,720] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:48:10,720] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:48:10,720] [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	78.5492	210	1234	95	below_threshold
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	77.9512	273	1234	95	below_threshold
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	77.1026	218	1234	95	below_threshold
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	76.1583	70	1234	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:48:10,762] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12971/tc_result.tsv
[2023-03-16 09:48:10,762] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:48:10,762] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:48:10,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference/checkm_data
[2023-03-16 09:48:10,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:48:10,771] [INFO] Task started: CheckM
[2023-03-16 09:48:10,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12971/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12971/checkm_input OceanDNA-b12971/checkm_result
[2023-03-16 09:49:15,955] [INFO] Task succeeded: CheckM
[2023-03-16 09:49:15,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:49:15,958] [INFO] ===== Completeness check finished =====
[2023-03-16 09:49:15,958] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:49:15,958] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12971/markers.fasta)
[2023-03-16 09:49:15,960] [INFO] Task started: Blastn
[2023-03-16 09:49:15,960] [INFO] Running command: blastn -query OceanDNA-b12971/markers.fasta -db /var/lib/cwl/stg651fbd6d-10b0-4e9f-9f49-04ea09cc0edf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12971/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:49:16,694] [INFO] Task succeeded: Blastn
[2023-03-16 09:49:16,695] [INFO] Selected 17 target genomes.
[2023-03-16 09:49:16,695] [INFO] Target genome list was writen to OceanDNA-b12971/target_genomes_gtdb.txt
[2023-03-16 09:49:16,707] [INFO] Task started: fastANI
[2023-03-16 09:49:16,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg574426a4-79e7-4d3a-b523-528121406f61/OceanDNA-b12971.fa --refList OceanDNA-b12971/target_genomes_gtdb.txt --output OceanDNA-b12971/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:49:26,083] [INFO] Task succeeded: fastANI
[2023-03-16 09:49:26,090] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:49:26,091] [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_002694685.1	s__Gracilimonas sp002694685	99.9979	1228	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	conclusive
GCA_017641085.1	s__Gracilimonas sp017641085	79.7705	470	1234	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	78.531	211	1234	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	78.5191	301	1234	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	78.0927	272	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900182705.1	s__Gracilimonas mengyeensis	77.1026	218	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711805.1	s__MES10 sp009711805	76.6989	133	1234	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	76.5332	93	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364085.1	s__Balneola sp002364085	76.3117	88	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
GCA_017643365.1	s__HXMU1420-13 sp017643365	76.1803	86	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375465.1	s__Balneola vulgaris	76.1583	70	1234	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:49:26,091] [INFO] GTDB search result was written to OceanDNA-b12971/result_gtdb.tsv
[2023-03-16 09:49:26,091] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:49:26,092] [INFO] DFAST_QC result json was written to OceanDNA-b12971/dqc_result.json
[2023-03-16 09:49:26,092] [INFO] DFAST_QC completed!
[2023-03-16 09:49:26,092] [INFO] Total running time: 0h1m55s