[2023-03-15 03:38:34,775] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:38:34,775] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:38:34,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference
[2023-03-15 03:38:35,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:38:35,898] [INFO] Task started: Prodigal
[2023-03-15 03:38:35,898] [INFO] Running command: cat /var/lib/cwl/stg1202b252-58e9-4268-9d52-1d11c2768688/OceanDNA-b2878.fa | prodigal -d OceanDNA-b2878/cds.fna -a OceanDNA-b2878/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:39:04,446] [INFO] Task succeeded: Prodigal
[2023-03-15 03:39:04,446] [INFO] Task started: HMMsearch
[2023-03-15 03:39:04,446] [INFO] Running command: hmmsearch --tblout OceanDNA-b2878/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference/reference_markers.hmm OceanDNA-b2878/protein.faa > /dev/null
[2023-03-15 03:39:04,682] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:39:04,683] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1202b252-58e9-4268-9d52-1d11c2768688/OceanDNA-b2878.fa]
[2023-03-15 03:39:04,721] [INFO] Query marker FASTA was written to OceanDNA-b2878/markers.fasta
[2023-03-15 03:39:04,723] [INFO] Task started: Blastn
[2023-03-15 03:39:04,723] [INFO] Running command: blastn -query OceanDNA-b2878/markers.fasta -db /var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference/reference_markers.fasta -out OceanDNA-b2878/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:39:08,412] [INFO] Task succeeded: Blastn
[2023-03-15 03:39:08,416] [INFO] Selected 15 target genomes.
[2023-03-15 03:39:08,416] [INFO] Target genome list was writen to OceanDNA-b2878/target_genomes.txt
[2023-03-15 03:39:08,475] [INFO] Task started: fastANI
[2023-03-15 03:39:08,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg1202b252-58e9-4268-9d52-1d11c2768688/OceanDNA-b2878.fa --refList OceanDNA-b2878/target_genomes.txt --output OceanDNA-b2878/fastani_result.tsv --threads 1
[2023-03-15 03:39:24,528] [INFO] Task succeeded: fastANI
[2023-03-15 03:39:24,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:39:24,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:39:24,538] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:39:24,538] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:39:24,538] [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
Rhodococcus fascians	strain=NBRC 12155	GCA_001894785.1	1828	1828	type	True	83.8792	1081	1483	95	below_threshold
Rhodococcus fascians	strain=LMG 3623	GCA_000761055.1	1828	1828	type	True	83.8077	1098	1483	95	below_threshold
Rhodococcus kyotonensis	strain=JCM 23211	GCA_900188125.1	398843	398843	type	True	79.5334	585	1483	95	below_threshold
Rhodococcus yunnanensis	strain=NBRC 103083	GCA_001895005.1	278209	278209	type	True	79.472	575	1483	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	78.1969	379	1483	95	below_threshold
Prescottella subtropica	strain=C9-28	GCA_005434945.1	2545757	2545757	type	True	78.1326	350	1483	95	below_threshold
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	78.0857	427	1483	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.0631	400	1483	95	below_threshold
Rhodococcus wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	78.0493	439	1483	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	77.5867	339	1483	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	77.566	344	1483	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	77.5153	348	1483	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	77.4553	338	1483	95	below_threshold
Rhodococcus marinonascens	strain=NBRC 14363	GCA_001894885.1	38311	38311	type	True	77.3522	284	1483	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	76.8799	180	1483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:39:24,539] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2878/tc_result.tsv
[2023-03-15 03:39:24,541] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:39:24,542] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:39:24,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference/checkm_data
[2023-03-15 03:39:24,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:39:24,557] [INFO] Task started: CheckM
[2023-03-15 03:39:24,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2878/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2878/checkm_input OceanDNA-b2878/checkm_result
[2023-03-15 03:40:35,674] [INFO] Task succeeded: CheckM
[2023-03-15 03:40:35,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.29%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 03:40:35,695] [INFO] ===== Completeness check finished =====
[2023-03-15 03:40:35,695] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:40:35,695] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2878/markers.fasta)
[2023-03-15 03:40:35,696] [INFO] Task started: Blastn
[2023-03-15 03:40:35,696] [INFO] Running command: blastn -query OceanDNA-b2878/markers.fasta -db /var/lib/cwl/stgf7eb83fc-29b8-4e4f-9260-4338172bf3ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2878/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:40:37,208] [INFO] Task succeeded: Blastn
[2023-03-15 03:40:37,212] [INFO] Selected 11 target genomes.
[2023-03-15 03:40:37,212] [INFO] Target genome list was writen to OceanDNA-b2878/target_genomes_gtdb.txt
[2023-03-15 03:40:37,265] [INFO] Task started: fastANI
[2023-03-15 03:40:37,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg1202b252-58e9-4268-9d52-1d11c2768688/OceanDNA-b2878.fa --refList OceanDNA-b2878/target_genomes_gtdb.txt --output OceanDNA-b2878/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:40:50,982] [INFO] Task succeeded: fastANI
[2023-03-15 03:40:50,989] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:40:50,990] [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
GCF_017168335.1	s__Rhodococcus_B sp017168335	98.5967	1390	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000333955.1	s__Rhodococcus_B sp000333955	86.8507	1147	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688915.1	s__Rhodococcus_B sp000813105	85.7314	1164	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.08	98.08	0.88	0.88	2	-
GCF_002259405.1	s__Rhodococcus_B sp002259405	85.4529	1131	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.16	0.87	0.86	5	-
GCF_002258785.1	s__Rhodococcus_B sp002258785	85.4485	1165	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258315.1	s__Rhodococcus_B sp002258315	85.3995	1148	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002259485.1	s__Rhodococcus_B sp002259485	85.2249	1143	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.08	96.72	0.90	0.88	8	-
GCF_000954115.1	s__Rhodococcus_B sp000954115	85.2034	1131	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.19	0.90	0.89	13	-
GCF_000760935.2	s__Rhodococcus_B sp002259335	85.1712	1149	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	96.52	96.34	0.85	0.83	9	-
GCF_001426085.1	s__Rhodococcus_B sp001426085	84.5935	1137	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168235.1	s__Rhodococcus_B sp001942265	80.6032	600	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.66	98.66	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:40:50,994] [INFO] GTDB search result was written to OceanDNA-b2878/result_gtdb.tsv
[2023-03-15 03:40:51,001] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:40:51,006] [INFO] DFAST_QC result json was written to OceanDNA-b2878/dqc_result.json
[2023-03-15 03:40:51,006] [INFO] DFAST_QC completed!
[2023-03-15 03:40:51,006] [INFO] Total running time: 0h2m16s