[2023-03-16 03:47:32,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference
[2023-03-16 03:47:34,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,536] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,536] [INFO] Running command: cat /var/lib/cwl/stg7b2a1beb-364c-46ff-a81b-32e1a4a9fa23/OceanDNA-b498.fa | prodigal -d OceanDNA-b498/cds.fna -a OceanDNA-b498/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:45,026] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:45,026] [INFO] Task started: HMMsearch
[2023-03-16 03:47:45,026] [INFO] Running command: hmmsearch --tblout OceanDNA-b498/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference/reference_markers.hmm OceanDNA-b498/protein.faa > /dev/null
[2023-03-16 03:47:45,271] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:45,271] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7b2a1beb-364c-46ff-a81b-32e1a4a9fa23/OceanDNA-b498.fa]
[2023-03-16 03:47:45,305] [INFO] Query marker FASTA was written to OceanDNA-b498/markers.fasta
[2023-03-16 03:47:45,305] [INFO] Task started: Blastn
[2023-03-16 03:47:45,305] [INFO] Running command: blastn -query OceanDNA-b498/markers.fasta -db /var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference/reference_markers.fasta -out OceanDNA-b498/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:45,926] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:45,927] [INFO] Selected 15 target genomes.
[2023-03-16 03:47:45,927] [INFO] Target genome list was writen to OceanDNA-b498/target_genomes.txt
[2023-03-16 03:47:45,935] [INFO] Task started: fastANI
[2023-03-16 03:47:45,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b2a1beb-364c-46ff-a81b-32e1a4a9fa23/OceanDNA-b498.fa --refList OceanDNA-b498/target_genomes.txt --output OceanDNA-b498/fastani_result.tsv --threads 1
[2023-03-16 03:47:57,886] [INFO] Task succeeded: fastANI
[2023-03-16 03:47:57,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:47:57,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:47:57,894] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:47:57,894] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:47:57,894] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	79.7661	322	502	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	78.8019	242	502	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.5345	235	502	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.507	221	502	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.0304	129	502	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	75.131	71	502	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	75.036	90	502	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	75.0071	95	502	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	74.9973	129	502	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	74.9773	91	502	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:47:57,895] [INFO] DFAST Taxonomy check result was written to OceanDNA-b498/tc_result.tsv
[2023-03-16 03:47:57,895] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:47:57,895] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:47:57,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference/checkm_data
[2023-03-16 03:47:57,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:47:57,901] [INFO] Task started: CheckM
[2023-03-16 03:47:57,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b498/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b498/checkm_input OceanDNA-b498/checkm_result
[2023-03-16 03:48:27,878] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:27,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:27,880] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:27,881] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:27,881] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b498/markers.fasta)
[2023-03-16 03:48:27,881] [INFO] Task started: Blastn
[2023-03-16 03:48:27,881] [INFO] Running command: blastn -query OceanDNA-b498/markers.fasta -db /var/lib/cwl/stgacd7ef48-b788-454d-b9ab-c8abf8a639dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b498/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:28,764] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:28,764] [INFO] Selected 15 target genomes.
[2023-03-16 03:48:28,764] [INFO] Target genome list was writen to OceanDNA-b498/target_genomes_gtdb.txt
[2023-03-16 03:48:28,802] [INFO] Task started: fastANI
[2023-03-16 03:48:28,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b2a1beb-364c-46ff-a81b-32e1a4a9fa23/OceanDNA-b498.fa --refList OceanDNA-b498/target_genomes_gtdb.txt --output OceanDNA-b498/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:38,694] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:38,703] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:38,703] [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_000348785.1	s__Ilumatobacter_A coccineus	79.7842	321	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	78.8201	241	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	78.0635	226	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815505.1	s__JACDHN01 sp013815505	77.1876	100	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024485.1	s__Casp-actino5 sp010024485	77.1443	69	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_013213745.1	s__JABSQH01 sp013213745	77.1359	142	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	77.1291	167	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	77.0993	191	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767405.1	s__Sva-07 sp015767405	76.4675	66	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	75.789	119	502	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388425.1	s__Nocardioides sp018388425	75.0707	68	502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.59	99.18	0.98	0.96	3	-
GCF_006494775.1	s__Nocardioides humi	74.9885	131	502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011299595.1	s__Marmoricola_A sp011299595	74.9595	71	502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087345.1	s__Marmoricola_A caldifontis	74.8989	91	502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	74.8338	94	502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:38,703] [INFO] GTDB search result was written to OceanDNA-b498/result_gtdb.tsv
[2023-03-16 03:48:38,703] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:38,705] [INFO] DFAST_QC result json was written to OceanDNA-b498/dqc_result.json
[2023-03-16 03:48:38,705] [INFO] DFAST_QC completed!
[2023-03-16 03:48:38,705] [INFO] Total running time: 0h1m6s