[2023-03-18 00:53:42,507] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference
[2023-03-18 00:53:43,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,648] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,648] [INFO] Running command: cat /var/lib/cwl/stgcaa2a4f9-aace-4753-8d1a-4acf81a40159/OceanDNA-b8032.fa | prodigal -d OceanDNA-b8032/cds.fna -a OceanDNA-b8032/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:53,019] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:53,019] [INFO] Task started: HMMsearch
[2023-03-18 00:53:53,019] [INFO] Running command: hmmsearch --tblout OceanDNA-b8032/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference/reference_markers.hmm OceanDNA-b8032/protein.faa > /dev/null
[2023-03-18 00:53:53,177] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:53,178] [INFO] Found 6/6 markers.
[2023-03-18 00:53:53,188] [INFO] Query marker FASTA was written to OceanDNA-b8032/markers.fasta
[2023-03-18 00:53:53,189] [INFO] Task started: Blastn
[2023-03-18 00:53:53,190] [INFO] Running command: blastn -query OceanDNA-b8032/markers.fasta -db /var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference/reference_markers.fasta -out OceanDNA-b8032/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:53,734] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:53,738] [INFO] Selected 35 target genomes.
[2023-03-18 00:53:53,738] [INFO] Target genome list was writen to OceanDNA-b8032/target_genomes.txt
[2023-03-18 00:53:53,758] [INFO] Task started: fastANI
[2023-03-18 00:53:53,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaa2a4f9-aace-4753-8d1a-4acf81a40159/OceanDNA-b8032.fa --refList OceanDNA-b8032/target_genomes.txt --output OceanDNA-b8032/fastani_result.tsv --threads 1
[2023-03-18 00:54:13,521] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:13,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:13,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:13,526] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:13,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:13,526] [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
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.8145	52	526	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	75.4695	55	526	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.4516	65	526	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	75.3702	59	526	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	75.3617	62	526	95	below_threshold
Tenacibaculum agarivorans	strain=HZ1	GCA_001936575.1	1908389	1908389	type	True	75.3166	57	526	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:13,532] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8032/tc_result.tsv
[2023-03-18 00:54:13,543] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:13,543] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:13,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference/checkm_data
[2023-03-18 00:54:13,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:13,571] [INFO] Task started: CheckM
[2023-03-18 00:54:13,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8032/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8032/checkm_input OceanDNA-b8032/checkm_result
[2023-03-18 00:54:41,368] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:41,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:41,387] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:41,387] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:41,387] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8032/markers.fasta)
[2023-03-18 00:54:41,389] [INFO] Task started: Blastn
[2023-03-18 00:54:41,389] [INFO] Running command: blastn -query OceanDNA-b8032/markers.fasta -db /var/lib/cwl/stg80881013-3370-49e6-ac2a-3725e11751a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8032/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:42,167] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:42,181] [INFO] Selected 16 target genomes.
[2023-03-18 00:54:42,181] [INFO] Target genome list was writen to OceanDNA-b8032/target_genomes_gtdb.txt
[2023-03-18 00:54:42,194] [INFO] Task started: fastANI
[2023-03-18 00:54:42,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaa2a4f9-aace-4753-8d1a-4acf81a40159/OceanDNA-b8032.fa --refList OceanDNA-b8032/target_genomes_gtdb.txt --output OceanDNA-b8032/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:46,802] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:46,811] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:54:46,811] [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_905181625.1	s__MAG-121220-bin8 sp905181625	99.667	516	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	82.0248	325	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	79.1295	207	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	78.7597	267	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	78.5115	213	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	78.1419	149	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	77.9756	186	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.8	211	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	77.797	210	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	77.7795	165	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.7759	166	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	77.7096	141	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	77.6891	143	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	77.4536	145	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
GCA_902597545.1	s__MED-G14 sp902597545	75.9426	65	526	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:46,817] [INFO] GTDB search result was written to OceanDNA-b8032/result_gtdb.tsv
[2023-03-18 00:54:46,824] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:46,830] [INFO] DFAST_QC result json was written to OceanDNA-b8032/dqc_result.json
[2023-03-18 00:54:46,831] [INFO] DFAST_QC completed!
[2023-03-18 00:54:46,831] [INFO] Total running time: 0h1m4s