[2023-06-29 20:05:45,108] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:05:45,115] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:05:45,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference
[2023-06-29 20:05:46,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:05:46,295] [INFO] Task started: Prodigal
[2023-06-29 20:05:46,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fe8991b-432b-4878-98c4-68c29e536d01/GCA_021202075.1_ASM2120207v1_genomic.fna.gz | prodigal -d GCA_021202075.1_ASM2120207v1_genomic.fna/cds.fna -a GCA_021202075.1_ASM2120207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:06:00,164] [INFO] Task succeeded: Prodigal
[2023-06-29 20:06:00,164] [INFO] Task started: HMMsearch
[2023-06-29 20:06:00,164] [INFO] Running command: hmmsearch --tblout GCA_021202075.1_ASM2120207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference/reference_markers.hmm GCA_021202075.1_ASM2120207v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:06:00,545] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:06:00,547] [INFO] Found 6/6 markers.
[2023-06-29 20:06:00,608] [INFO] Query marker FASTA was written to GCA_021202075.1_ASM2120207v1_genomic.fna/markers.fasta
[2023-06-29 20:06:00,609] [INFO] Task started: Blastn
[2023-06-29 20:06:00,609] [INFO] Running command: blastn -query GCA_021202075.1_ASM2120207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference/reference_markers.fasta -out GCA_021202075.1_ASM2120207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:06:01,356] [INFO] Task succeeded: Blastn
[2023-06-29 20:06:01,360] [INFO] Selected 28 target genomes.
[2023-06-29 20:06:01,361] [INFO] Target genome list was writen to GCA_021202075.1_ASM2120207v1_genomic.fna/target_genomes.txt
[2023-06-29 20:06:01,362] [INFO] Task started: fastANI
[2023-06-29 20:06:01,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe8991b-432b-4878-98c4-68c29e536d01/GCA_021202075.1_ASM2120207v1_genomic.fna.gz --refList GCA_021202075.1_ASM2120207v1_genomic.fna/target_genomes.txt --output GCA_021202075.1_ASM2120207v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:06:18,377] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:18,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:06:18,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:06:18,387] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:06:18,387] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:06:18,388] [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
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.6895	129	1770	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.638	134	1770	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.5605	132	1770	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	75.866	64	1770	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	75.8517	75	1770	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:06:18,390] [INFO] DFAST Taxonomy check result was written to GCA_021202075.1_ASM2120207v1_genomic.fna/tc_result.tsv
[2023-06-29 20:06:18,391] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:06:18,391] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:06:18,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference/checkm_data
[2023-06-29 20:06:18,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:06:18,449] [INFO] Task started: CheckM
[2023-06-29 20:06:18,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021202075.1_ASM2120207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021202075.1_ASM2120207v1_genomic.fna/checkm_input GCA_021202075.1_ASM2120207v1_genomic.fna/checkm_result
[2023-06-29 20:07:03,231] [INFO] Task succeeded: CheckM
[2023-06-29 20:07:03,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:07:03,258] [INFO] ===== Completeness check finished =====
[2023-06-29 20:07:03,258] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:07:03,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021202075.1_ASM2120207v1_genomic.fna/markers.fasta)
[2023-06-29 20:07:03,259] [INFO] Task started: Blastn
[2023-06-29 20:07:03,259] [INFO] Running command: blastn -query GCA_021202075.1_ASM2120207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93376a37-6ad6-4d5f-a8b9-b0c933beb92d/dqc_reference/reference_markers_gtdb.fasta -out GCA_021202075.1_ASM2120207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:07:04,421] [INFO] Task succeeded: Blastn
[2023-06-29 20:07:04,426] [INFO] Selected 25 target genomes.
[2023-06-29 20:07:04,427] [INFO] Target genome list was writen to GCA_021202075.1_ASM2120207v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:07:04,497] [INFO] Task started: fastANI
[2023-06-29 20:07:04,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe8991b-432b-4878-98c4-68c29e536d01/GCA_021202075.1_ASM2120207v1_genomic.fna.gz --refList GCA_021202075.1_ASM2120207v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021202075.1_ASM2120207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:07:17,021] [INFO] Task succeeded: fastANI
[2023-06-29 20:07:17,047] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:07:17,047] [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_001941045.1	s__Choladocola sp001941045	77.7236	130	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363135.1	s__Choladousia sp902363135	76.93	150	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_004557975.1	s__Choladousia sp004557975	76.9143	123	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201705.1	s__Marvinbryantia sp900550755	76.8571	109	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.85	99.71	0.93	0.91	3	-
GCA_002491565.1	s__Choladousia sp002491565	76.8276	162	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173815.1	s__Marvinbryantia formatexigens	76.6895	129	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.98	99.98	0.99	0.99	3	-
GCA_003612585.1	s__Choladousia sp003612585	76.6706	116	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363665.1	s__Choladousia sp902363665	76.6139	127	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCA_018713105.1	s__Limivivens merdigallinarum	76.6089	59	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.32	98.32	0.87	0.87	2	-
GCA_018712605.1	s__Choladousia intestinigallinarum	76.4216	75	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.46	98.46	0.75	0.75	2	-
GCA_019117125.1	s__Mediterraneibacter merdipullorum	76.3904	54	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711885.1	s__Choladousia intestinipullorum	76.3899	94	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713435.1	s__Merdiplasma excrementigallinarum	76.3146	69	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712785.1	s__Choladousia intestinavium	76.045	93	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.61	98.61	0.86	0.86	2	-
GCA_910584725.1	s__UBA3282 sp910584725	75.9501	65	1770	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:07:17,049] [INFO] GTDB search result was written to GCA_021202075.1_ASM2120207v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:07:17,050] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:07:17,053] [INFO] DFAST_QC result json was written to GCA_021202075.1_ASM2120207v1_genomic.fna/dqc_result.json
[2023-06-29 20:07:17,053] [INFO] DFAST_QC completed!
[2023-06-29 20:07:17,053] [INFO] Total running time: 0h1m32s