[2023-03-17 09:07:11,233] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:07:11,233] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:07:11,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference
[2023-03-17 09:07:12,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:07:12,320] [INFO] Task started: Prodigal
[2023-03-17 09:07:12,320] [INFO] Running command: cat /var/lib/cwl/stgce0ba6cd-209a-46c2-b0b3-4c3d2aa66971/OceanDNA-b12878.fa | prodigal -d OceanDNA-b12878/cds.fna -a OceanDNA-b12878/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:07:35,539] [INFO] Task succeeded: Prodigal
[2023-03-17 09:07:35,539] [INFO] Task started: HMMsearch
[2023-03-17 09:07:35,539] [INFO] Running command: hmmsearch --tblout OceanDNA-b12878/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference/reference_markers.hmm OceanDNA-b12878/protein.faa > /dev/null
[2023-03-17 09:07:35,770] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:07:35,771] [INFO] Found 6/6 markers.
[2023-03-17 09:07:35,793] [INFO] Query marker FASTA was written to OceanDNA-b12878/markers.fasta
[2023-03-17 09:07:35,794] [INFO] Task started: Blastn
[2023-03-17 09:07:35,794] [INFO] Running command: blastn -query OceanDNA-b12878/markers.fasta -db /var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference/reference_markers.fasta -out OceanDNA-b12878/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:07:36,348] [INFO] Task succeeded: Blastn
[2023-03-17 09:07:36,348] [INFO] Selected 21 target genomes.
[2023-03-17 09:07:36,349] [INFO] Target genome list was writen to OceanDNA-b12878/target_genomes.txt
[2023-03-17 09:07:36,851] [INFO] Task started: fastANI
[2023-03-17 09:07:36,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgce0ba6cd-209a-46c2-b0b3-4c3d2aa66971/OceanDNA-b12878.fa --refList OceanDNA-b12878/target_genomes.txt --output OceanDNA-b12878/fastani_result.tsv --threads 1
[2023-03-17 09:07:51,140] [INFO] Task succeeded: fastANI
[2023-03-17 09:07:51,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:07:51,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:07:51,151] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:07:51,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:07:51,151] [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
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	78.3961	436	1166	95	below_threshold
Pedobacter arcticus	strain=A12	GCA_000302595.1	752140	752140	type	True	78.1925	234	1166	95	below_threshold
Pedobacter psychrophilus	strain=CCM 8644	GCA_001652725.1	1826909	1826909	type	True	78.1838	364	1166	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	77.6454	282	1166	95	below_threshold
Pedobacter glucosidilyticus	strain=DSM 23534	GCA_000425145.1	1122941	1122941	type	True	77.3857	228	1166	95	below_threshold
Pedobacter puniceum	strain=HX-22-1	GCA_009674685.1	2666136	2666136	type	True	77.3606	237	1166	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	77.3299	238	1166	95	below_threshold
Pseudopedobacter saltans	strain=DSM 12145	GCA_000190735.2	151895	151895	type	True	77.0427	99	1166	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.5873	76	1166	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	76.4355	119	1166	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	76.3925	95	1166	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	76.3816	57	1166	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	76.2461	57	1166	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	76.2356	114	1166	95	below_threshold
Pedobacter changchengzhani	strain=E01020	GCA_004354365.1	2529274	2529274	type	True	76.2186	93	1166	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	76.0332	64	1166	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.0151	63	1166	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:07:51,151] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12878/tc_result.tsv
[2023-03-17 09:07:51,151] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:07:51,152] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:07:51,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference/checkm_data
[2023-03-17 09:07:51,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:07:51,157] [INFO] Task started: CheckM
[2023-03-17 09:07:51,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12878/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12878/checkm_input OceanDNA-b12878/checkm_result
[2023-03-17 09:08:53,884] [INFO] Task succeeded: CheckM
[2023-03-17 09:08:53,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:08:53,887] [INFO] ===== Completeness check finished =====
[2023-03-17 09:08:53,887] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:08:53,887] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12878/markers.fasta)
[2023-03-17 09:08:53,889] [INFO] Task started: Blastn
[2023-03-17 09:08:53,889] [INFO] Running command: blastn -query OceanDNA-b12878/markers.fasta -db /var/lib/cwl/stg66cc1153-6717-4b97-b6fd-0e2ee18e6b12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12878/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:08:55,034] [INFO] Task succeeded: Blastn
[2023-03-17 09:08:55,034] [INFO] Selected 14 target genomes.
[2023-03-17 09:08:55,035] [INFO] Target genome list was writen to OceanDNA-b12878/target_genomes_gtdb.txt
[2023-03-17 09:08:55,284] [INFO] Task started: fastANI
[2023-03-17 09:08:55,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgce0ba6cd-209a-46c2-b0b3-4c3d2aa66971/OceanDNA-b12878.fa --refList OceanDNA-b12878/target_genomes_gtdb.txt --output OceanDNA-b12878/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:09:04,607] [INFO] Task succeeded: fastANI
[2023-03-17 09:09:04,615] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:09:04,616] [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_018828585.1	s__Pelobium sp018828585	99.9244	1084	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	99.93	99.87	0.97	0.95	6	conclusive
GCA_014378105.1	s__Pelobium sp014378105	93.609	818	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763615.1	s__Pelobium sp014763615	79.1998	497	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378285.1	s__Pelobium sp014378285	78.4276	191	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116455.1	s__Pelobium sp005116455	78.3925	437	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652725.1	s__Pelobium psychrophilum	78.1935	363	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302595.1	s__Pelobium arcticum	78.1925	234	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483235.1	s__Pelobium glucosidilyticum_B	77.7015	203	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425145.1	s__Pelobium glucosidilyticum	77.3831	229	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799115.1	s__Pelobium glucosidilyticum_A	77.2801	233	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
GCA_004292865.1	s__Pelobium sp004292865	77.0214	70	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	76.4557	119	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736205.1	s__Pedobacter ginsengisoli	76.4192	89	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306625.1	s__Pedobacter sp014306625	76.2553	114	1166	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:09:04,616] [INFO] GTDB search result was written to OceanDNA-b12878/result_gtdb.tsv
[2023-03-17 09:09:04,616] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:09:04,618] [INFO] DFAST_QC result json was written to OceanDNA-b12878/dqc_result.json
[2023-03-17 09:09:04,618] [INFO] DFAST_QC completed!
[2023-03-17 09:09:04,618] [INFO] Total running time: 0h1m53s