[2023-03-17 04:48:54,044] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,044] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference
[2023-03-17 04:48:55,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,243] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,243] [INFO] Running command: cat /var/lib/cwl/stg6be01816-ffae-4cbe-8e07-30e317541113/OceanDNA-b2880.fa | prodigal -d OceanDNA-b2880/cds.fna -a OceanDNA-b2880/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:12,458] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:12,459] [INFO] Task started: HMMsearch
[2023-03-17 04:49:12,459] [INFO] Running command: hmmsearch --tblout OceanDNA-b2880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference/reference_markers.hmm OceanDNA-b2880/protein.faa > /dev/null
[2023-03-17 04:49:12,654] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:12,654] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6be01816-ffae-4cbe-8e07-30e317541113/OceanDNA-b2880.fa]
[2023-03-17 04:49:12,681] [INFO] Query marker FASTA was written to OceanDNA-b2880/markers.fasta
[2023-03-17 04:49:12,681] [INFO] Task started: Blastn
[2023-03-17 04:49:12,681] [INFO] Running command: blastn -query OceanDNA-b2880/markers.fasta -db /var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference/reference_markers.fasta -out OceanDNA-b2880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:13,311] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:13,311] [INFO] Selected 10 target genomes.
[2023-03-17 04:49:13,312] [INFO] Target genome list was writen to OceanDNA-b2880/target_genomes.txt
[2023-03-17 04:49:13,317] [INFO] Task started: fastANI
[2023-03-17 04:49:13,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg6be01816-ffae-4cbe-8e07-30e317541113/OceanDNA-b2880.fa --refList OceanDNA-b2880/target_genomes.txt --output OceanDNA-b2880/fastani_result.tsv --threads 1
[2023-03-17 04:49:23,335] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:23,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:23,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:23,343] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 04:49:23,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 04:49:23,343] [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=LMG 3623	GCA_000761055.1	1828	1828	type	True	97.6523	762	833	95	conclusive
Rhodococcus fascians	strain=NBRC 12155	GCA_001894785.1	1828	1828	type	True	97.6377	765	833	95	conclusive
Rhodococcus kyotonensis	strain=JCM 23211	GCA_900188125.1	398843	398843	type	True	79.581	388	833	95	below_threshold
Rhodococcus yunnanensis	strain=NBRC 103083	GCA_001895005.1	278209	278209	type	True	79.3459	371	833	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	78.1221	285	833	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.1169	247	833	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	77.9147	264	833	95	below_threshold
Rhodococcus erythropolis	strain=DSM 43066	GCA_022134675.1	1833	1833	type	True	77.9145	220	833	95	below_threshold
Rhodococcus cavernicola	strain=C1-24	GCA_008297975.1	2495913	2495913	type	True	77.4848	200	833	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	76.9927	159	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:49:23,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2880/tc_result.tsv
[2023-03-17 04:49:23,343] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:23,343] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:23,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference/checkm_data
[2023-03-17 04:49:23,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:23,349] [INFO] Task started: CheckM
[2023-03-17 04:49:23,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2880/checkm_input OceanDNA-b2880/checkm_result
[2023-03-17 04:50:08,064] [INFO] Task succeeded: CheckM
[2023-03-17 04:50:08,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:50:08,067] [INFO] ===== Completeness check finished =====
[2023-03-17 04:50:08,067] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:50:08,067] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2880/markers.fasta)
[2023-03-17 04:50:08,069] [INFO] Task started: Blastn
[2023-03-17 04:50:08,069] [INFO] Running command: blastn -query OceanDNA-b2880/markers.fasta -db /var/lib/cwl/stg6dea19b0-789f-470f-ad68-b031c8801347/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:50:08,805] [INFO] Task succeeded: Blastn
[2023-03-17 04:50:08,806] [INFO] Selected 8 target genomes.
[2023-03-17 04:50:08,806] [INFO] Target genome list was writen to OceanDNA-b2880/target_genomes_gtdb.txt
[2023-03-17 04:50:08,843] [INFO] Task started: fastANI
[2023-03-17 04:50:08,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg6be01816-ffae-4cbe-8e07-30e317541113/OceanDNA-b2880.fa --refList OceanDNA-b2880/target_genomes_gtdb.txt --output OceanDNA-b2880/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:17,794] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:17,800] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:50:17,800] [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_001894785.1	s__Rhodococcus_B fascians	97.6377	765	833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	97.73	95.09	0.88	0.82	43	conclusive
GCF_000760935.2	s__Rhodococcus_B sp002259335	85.5028	684	833	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_002259405.1	s__Rhodococcus_B sp002259405	84.9873	688	833	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_003688915.1	s__Rhodococcus_B sp000813105	84.9377	657	833	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_002259485.1	s__Rhodococcus_B sp002259485	84.8076	662	833	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	84.7753	661	833	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_002258315.1	s__Rhodococcus_B sp002258315	84.7689	674	833	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_000333955.1	s__Rhodococcus_B sp000333955	84.1694	645	833	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:17,800] [INFO] GTDB search result was written to OceanDNA-b2880/result_gtdb.tsv
[2023-03-17 04:50:17,800] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:17,801] [INFO] DFAST_QC result json was written to OceanDNA-b2880/dqc_result.json
[2023-03-17 04:50:17,801] [INFO] DFAST_QC completed!
[2023-03-17 04:50:17,801] [INFO] Total running time: 0h1m24s