[2023-06-08 03:42:22,501] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:22,505] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:22,505] [INFO] DQC Reference Directory: /var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference
[2023-06-08 03:42:23,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:23,937] [INFO] Task started: Prodigal
[2023-06-08 03:42:23,937] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf690224-59e2-4620-8915-a3ba5d203342/GCA_945903585.1_TrH-03may19-155_genomic.fna.gz | prodigal -d GCA_945903585.1_TrH-03may19-155_genomic.fna/cds.fna -a GCA_945903585.1_TrH-03may19-155_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:37,219] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:37,220] [INFO] Task started: HMMsearch
[2023-06-08 03:42:37,220] [INFO] Running command: hmmsearch --tblout GCA_945903585.1_TrH-03may19-155_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference/reference_markers.hmm GCA_945903585.1_TrH-03may19-155_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:37,537] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:37,538] [INFO] Found 6/6 markers.
[2023-06-08 03:42:37,586] [INFO] Query marker FASTA was written to GCA_945903585.1_TrH-03may19-155_genomic.fna/markers.fasta
[2023-06-08 03:42:37,586] [INFO] Task started: Blastn
[2023-06-08 03:42:37,587] [INFO] Running command: blastn -query GCA_945903585.1_TrH-03may19-155_genomic.fna/markers.fasta -db /var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference/reference_markers.fasta -out GCA_945903585.1_TrH-03may19-155_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:38,206] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:38,210] [INFO] Selected 30 target genomes.
[2023-06-08 03:42:38,210] [INFO] Target genome list was writen to GCA_945903585.1_TrH-03may19-155_genomic.fna/target_genomes.txt
[2023-06-08 03:42:38,215] [INFO] Task started: fastANI
[2023-06-08 03:42:38,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf690224-59e2-4620-8915-a3ba5d203342/GCA_945903585.1_TrH-03may19-155_genomic.fna.gz --refList GCA_945903585.1_TrH-03may19-155_genomic.fna/target_genomes.txt --output GCA_945903585.1_TrH-03may19-155_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:42:59,989] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:59,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:42:59,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:42:59,997] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:42:59,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:42:59,997] [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
Bryobacter aggregatus	strain=MPL3	GCA_000702445.1	360054	360054	type	True	75.8928	69	1421	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.0185	62	1421	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.6994	55	1421	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.6764	54	1421	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.6594	58	1421	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	74.5955	52	1421	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	74.5915	53	1421	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:42:59,999] [INFO] DFAST Taxonomy check result was written to GCA_945903585.1_TrH-03may19-155_genomic.fna/tc_result.tsv
[2023-06-08 03:42:59,999] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:43:00,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:43:00,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference/checkm_data
[2023-06-08 03:43:00,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:43:00,042] [INFO] Task started: CheckM
[2023-06-08 03:43:00,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945903585.1_TrH-03may19-155_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945903585.1_TrH-03may19-155_genomic.fna/checkm_input GCA_945903585.1_TrH-03may19-155_genomic.fna/checkm_result
[2023-06-08 03:43:40,191] [INFO] Task succeeded: CheckM
[2023-06-08 03:43:40,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:43:40,211] [INFO] ===== Completeness check finished =====
[2023-06-08 03:43:40,212] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:43:40,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945903585.1_TrH-03may19-155_genomic.fna/markers.fasta)
[2023-06-08 03:43:40,212] [INFO] Task started: Blastn
[2023-06-08 03:43:40,212] [INFO] Running command: blastn -query GCA_945903585.1_TrH-03may19-155_genomic.fna/markers.fasta -db /var/lib/cwl/stgef2c036b-dead-4513-9b40-725506f28fba/dqc_reference/reference_markers_gtdb.fasta -out GCA_945903585.1_TrH-03may19-155_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:43:41,099] [INFO] Task succeeded: Blastn
[2023-06-08 03:43:41,121] [INFO] Selected 33 target genomes.
[2023-06-08 03:43:41,121] [INFO] Target genome list was writen to GCA_945903585.1_TrH-03may19-155_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:43:41,197] [INFO] Task started: fastANI
[2023-06-08 03:43:41,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf690224-59e2-4620-8915-a3ba5d203342/GCA_945903585.1_TrH-03may19-155_genomic.fna.gz --refList GCA_945903585.1_TrH-03may19-155_genomic.fna/target_genomes_gtdb.txt --output GCA_945903585.1_TrH-03may19-155_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:44:06,902] [INFO] Task succeeded: fastANI
[2023-06-08 03:44:06,925] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 03:44:06,925] [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_902826605.1	s__Palsa-187 sp902826605	76.7636	85	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892565.1	s__Palsa-187 sp903892565	76.4121	119	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697505.1	s__Palsa-187 sp009697505	76.334	106	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170295.1	s__Palsa-187 sp003170295	76.2923	89	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-187	95.0	99.79	99.79	0.87	0.87	2	-
GCA_903925975.1	s__BOG-224 sp903925975	76.1772	63	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789905.1	s__Ga0077553 sp016789905	76.1368	80	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Ga0077553	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860455.1	s__PNKE01 sp014860455	76.0607	77	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PNKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167255.1	s__PALSA-129 sp003167255	75.9989	79	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-129	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268835.1	s__Solibacter sp018268835	75.9883	125	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871115.1	s__DSOI01 sp016871115	75.9663	105	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__DSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871155.1	s__Ga0077553 sp016871155	75.9326	77	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Ga0077553	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907865.1	s__BOG-234 sp903907865	75.837	111	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-234	95.0	99.99	99.99	0.99	0.98	3	-
GCA_903881085.1	s__CAIRSA01 sp903881085	75.8136	106	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CAIRSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135055.1	s__PALSA-243 sp003135055	75.785	108	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-243	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139735.1	s__BOG-224 sp003139735	75.7779	59	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019261985.1	s__Palsa-187 sp019261985	75.6702	111	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-187	95.0	99.77	99.77	0.89	0.89	2	-
GCA_002298225.1	s__Paludibaculum sp002298225	75.6258	85	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Paludibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003166475.1	s__Bog-159 sp003166475	75.5915	89	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-159	95.0	99.58	99.43	0.89	0.86	9	-
GCA_016213755.1	s__JACQZT01 sp016213755	75.5357	113	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JACQZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132905.1	s__Palsa-89 sp003132905	75.5255	50	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003154855.1	s__Fen-330 sp003154855	75.5122	60	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Fen-330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136215.1	s__Solibacter sp003136215	75.2523	86	1421	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	99.46	99.46	0.86	0.86	2	-
GCF_001571085.1	s__Azohydromonas lata	74.6994	55	1421	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:44:06,927] [INFO] GTDB search result was written to GCA_945903585.1_TrH-03may19-155_genomic.fna/result_gtdb.tsv
[2023-06-08 03:44:06,927] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:44:06,931] [INFO] DFAST_QC result json was written to GCA_945903585.1_TrH-03may19-155_genomic.fna/dqc_result.json
[2023-06-08 03:44:06,931] [INFO] DFAST_QC completed!
[2023-06-08 03:44:06,931] [INFO] Total running time: 0h1m44s