[2023-06-29 18:14:01,443] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:14:01,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:14:01,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference
[2023-06-29 18:14:05,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:14:05,229] [INFO] Task started: Prodigal
[2023-06-29 18:14:05,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg2930b9e7-7e03-4c90-8cd1-132eaac0299f/GCA_910586485.1_MGBC141809_genomic.fna.gz | prodigal -d GCA_910586485.1_MGBC141809_genomic.fna/cds.fna -a GCA_910586485.1_MGBC141809_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:14:15,376] [INFO] Task succeeded: Prodigal
[2023-06-29 18:14:15,377] [INFO] Task started: HMMsearch
[2023-06-29 18:14:15,377] [INFO] Running command: hmmsearch --tblout GCA_910586485.1_MGBC141809_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference/reference_markers.hmm GCA_910586485.1_MGBC141809_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:14:15,704] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:14:15,705] [INFO] Found 6/6 markers.
[2023-06-29 18:14:15,741] [INFO] Query marker FASTA was written to GCA_910586485.1_MGBC141809_genomic.fna/markers.fasta
[2023-06-29 18:14:15,742] [INFO] Task started: Blastn
[2023-06-29 18:14:15,742] [INFO] Running command: blastn -query GCA_910586485.1_MGBC141809_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference/reference_markers.fasta -out GCA_910586485.1_MGBC141809_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:14:16,430] [INFO] Task succeeded: Blastn
[2023-06-29 18:14:16,434] [INFO] Selected 28 target genomes.
[2023-06-29 18:14:16,435] [INFO] Target genome list was writen to GCA_910586485.1_MGBC141809_genomic.fna/target_genomes.txt
[2023-06-29 18:14:16,440] [INFO] Task started: fastANI
[2023-06-29 18:14:16,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg2930b9e7-7e03-4c90-8cd1-132eaac0299f/GCA_910586485.1_MGBC141809_genomic.fna.gz --refList GCA_910586485.1_MGBC141809_genomic.fna/target_genomes.txt --output GCA_910586485.1_MGBC141809_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:14:34,317] [INFO] Task succeeded: fastANI
[2023-06-29 18:14:34,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:14:34,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:14:34,332] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:14:34,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 18:14:34,333] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.9559	206	1249	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.4427	85	1249	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.2308	91	1249	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	75.809	51	1249	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	75.7056	53	1249	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	75.7038	54	1249	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	75.6795	53	1249	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:14:34,335] [INFO] DFAST Taxonomy check result was written to GCA_910586485.1_MGBC141809_genomic.fna/tc_result.tsv
[2023-06-29 18:14:34,336] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:14:34,336] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:14:34,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference/checkm_data
[2023-06-29 18:14:34,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:14:34,380] [INFO] Task started: CheckM
[2023-06-29 18:14:34,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910586485.1_MGBC141809_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910586485.1_MGBC141809_genomic.fna/checkm_input GCA_910586485.1_MGBC141809_genomic.fna/checkm_result
[2023-06-29 18:15:08,077] [INFO] Task succeeded: CheckM
[2023-06-29 18:15:08,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:15:08,101] [INFO] ===== Completeness check finished =====
[2023-06-29 18:15:08,101] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:15:08,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910586485.1_MGBC141809_genomic.fna/markers.fasta)
[2023-06-29 18:15:08,102] [INFO] Task started: Blastn
[2023-06-29 18:15:08,102] [INFO] Running command: blastn -query GCA_910586485.1_MGBC141809_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df40ce0-5f20-4278-96ff-4e846942249b/dqc_reference/reference_markers_gtdb.fasta -out GCA_910586485.1_MGBC141809_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:15:09,204] [INFO] Task succeeded: Blastn
[2023-06-29 18:15:09,209] [INFO] Selected 14 target genomes.
[2023-06-29 18:15:09,210] [INFO] Target genome list was writen to GCA_910586485.1_MGBC141809_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:15:09,219] [INFO] Task started: fastANI
[2023-06-29 18:15:09,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg2930b9e7-7e03-4c90-8cd1-132eaac0299f/GCA_910586485.1_MGBC141809_genomic.fna.gz --refList GCA_910586485.1_MGBC141809_genomic.fna/target_genomes_gtdb.txt --output GCA_910586485.1_MGBC141809_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:15:18,879] [INFO] Task succeeded: fastANI
[2023-06-29 18:15:18,895] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:15:18,896] [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_910586485.1	s__Acetatifactor sp910586485	100.0	1242	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910578815.1	s__Acetatifactor sp910578815	90.6008	1007	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577035.1	s__Acetatifactor sp910577035	81.345	712	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586835.1	s__Acetatifactor sp910586835	78.1108	350	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583845.1	s__Acetatifactor sp910583845	77.7254	214	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755865.1	s__Acetatifactor sp900755865	77.4248	120	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.03	98.03	0.82	0.82	2	-
GCA_016303085.1	s__Acetatifactor sp016303085	77.3608	197	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554205.1	s__Acetatifactor sp900554205	77.2653	218	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.93	99.93	0.88	0.88	2	-
GCA_019114005.1	s__Acetatifactor stercoripullorum	77.0797	204	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.97	99.97	0.97	0.97	2	-
GCA_910577235.1	s__Acetatifactor sp910577235	76.7092	167	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009177215.1	s__Acetatifactor sp009177215	76.5478	131	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587555.1	s__Acetatifactor sp910587555	76.5089	170	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461775.1	s__Acetatifactor sp017461775	75.9524	61	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492295.1	s__COE1 sp002492295	75.3847	52	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:15:18,898] [INFO] GTDB search result was written to GCA_910586485.1_MGBC141809_genomic.fna/result_gtdb.tsv
[2023-06-29 18:15:18,899] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:15:18,904] [INFO] DFAST_QC result json was written to GCA_910586485.1_MGBC141809_genomic.fna/dqc_result.json
[2023-06-29 18:15:18,905] [INFO] DFAST_QC completed!
[2023-06-29 18:15:18,905] [INFO] Total running time: 0h1m17s