[2023-03-15 22:48:49,200] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:48:49,200] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:48:49,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference
[2023-03-15 22:48:50,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:48:50,321] [INFO] Task started: Prodigal
[2023-03-15 22:48:50,321] [INFO] Running command: cat /var/lib/cwl/stg8690955d-9c70-4da8-a50a-85026f23652c/OceanDNA-b1117.fa | prodigal -d OceanDNA-b1117/cds.fna -a OceanDNA-b1117/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:49:02,554] [INFO] Task succeeded: Prodigal
[2023-03-15 22:49:02,554] [INFO] Task started: HMMsearch
[2023-03-15 22:49:02,554] [INFO] Running command: hmmsearch --tblout OceanDNA-b1117/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference/reference_markers.hmm OceanDNA-b1117/protein.faa > /dev/null
[2023-03-15 22:49:02,727] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:49:02,727] [INFO] Found 6/6 markers.
[2023-03-15 22:49:02,746] [INFO] Query marker FASTA was written to OceanDNA-b1117/markers.fasta
[2023-03-15 22:49:02,748] [INFO] Task started: Blastn
[2023-03-15 22:49:02,748] [INFO] Running command: blastn -query OceanDNA-b1117/markers.fasta -db /var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference/reference_markers.fasta -out OceanDNA-b1117/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:49:03,379] [INFO] Task succeeded: Blastn
[2023-03-15 22:49:03,380] [INFO] Selected 26 target genomes.
[2023-03-15 22:49:03,380] [INFO] Target genome list was writen to OceanDNA-b1117/target_genomes.txt
[2023-03-15 22:49:03,538] [INFO] Task started: fastANI
[2023-03-15 22:49:03,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg8690955d-9c70-4da8-a50a-85026f23652c/OceanDNA-b1117.fa --refList OceanDNA-b1117/target_genomes.txt --output OceanDNA-b1117/fastani_result.tsv --threads 1
[2023-03-15 22:49:20,316] [INFO] Task succeeded: fastANI
[2023-03-15 22:49:20,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:49:20,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:49:20,327] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:49:20,327] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:49:20,327] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.9647	150	645	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.8216	160	645	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.7763	121	645	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.0019	81	645	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8751	129	645	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.7449	106	645	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.6673	82	645	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	75.375	58	645	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	75.3572	70	645	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	75.3009	55	645	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	75.2871	69	645	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	75.2846	63	645	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	75.2794	63	645	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	75.2366	63	645	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	75.1554	81	645	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	75.0698	56	645	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:49:20,328] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1117/tc_result.tsv
[2023-03-15 22:49:20,328] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:49:20,328] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:49:20,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference/checkm_data
[2023-03-15 22:49:20,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:49:20,332] [INFO] Task started: CheckM
[2023-03-15 22:49:20,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1117/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1117/checkm_input OceanDNA-b1117/checkm_result
[2023-03-15 22:49:54,080] [INFO] Task succeeded: CheckM
[2023-03-15 22:49:54,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:49:54,093] [INFO] ===== Completeness check finished =====
[2023-03-15 22:49:54,093] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:49:54,093] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1117/markers.fasta)
[2023-03-15 22:49:54,094] [INFO] Task started: Blastn
[2023-03-15 22:49:54,094] [INFO] Running command: blastn -query OceanDNA-b1117/markers.fasta -db /var/lib/cwl/stg03dab99d-03a7-4f73-ba2d-a48606b1aed5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1117/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:49:55,060] [INFO] Task succeeded: Blastn
[2023-03-15 22:49:55,062] [INFO] Selected 15 target genomes.
[2023-03-15 22:49:55,062] [INFO] Target genome list was writen to OceanDNA-b1117/target_genomes_gtdb.txt
[2023-03-15 22:49:55,529] [INFO] Task started: fastANI
[2023-03-15 22:49:55,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg8690955d-9c70-4da8-a50a-85026f23652c/OceanDNA-b1117.fa --refList OceanDNA-b1117/target_genomes_gtdb.txt --output OceanDNA-b1117/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:50:02,525] [INFO] Task succeeded: fastANI
[2023-03-15 22:50:02,533] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:50:02,533] [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_015658775.1	s__UBA3125 sp015658775	98.7475	488	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	conclusive
GCA_002346745.1	s__S20-B6 sp002346745	79.6088	333	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_016845305.1	s__UBA9410 sp016845305	79.5536	356	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673475.1	s__UBA3125 sp018673475	79.1984	316	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.96	99.93	0.97	0.96	16	-
GCA_002687745.1	s__UBA3125 sp002687745	79.1424	276	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.98	96.61	0.89	0.87	5	-
GCA_014381945.1	s__S20-B6 sp014381945	78.9536	345	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	78.9506	317	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002329075.1	s__S20-B6 sp002329075	78.8527	325	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_002365325.1	s__UBA3125 sp002365325	78.7782	255	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
GCA_014239855.1	s__UBA9410 sp014239855	78.7259	310	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501135.1	s__UBA3125 sp002501135	78.6524	288	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	99.79	99.79	0.86	0.86	2	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	76.4957	120	645	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635045.1	s__Terracoccus luteus	75.3652	61	645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	98.59	98.59	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:50:02,534] [INFO] GTDB search result was written to OceanDNA-b1117/result_gtdb.tsv
[2023-03-15 22:50:02,535] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:50:02,539] [INFO] DFAST_QC result json was written to OceanDNA-b1117/dqc_result.json
[2023-03-15 22:50:02,539] [INFO] DFAST_QC completed!
[2023-03-15 22:50:02,540] [INFO] Total running time: 0h1m13s