[2024-01-24 11:52:04,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference
[2024-01-24 11:52:06,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:06,005] [INFO] Task started: Prodigal
[2024-01-24 11:52:06,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d4e74a1-3a9e-4c78-8903-5b8a8a655273/GCF_019355395.1_ASM1935539v1_genomic.fna.gz | prodigal -d GCF_019355395.1_ASM1935539v1_genomic.fna/cds.fna -a GCF_019355395.1_ASM1935539v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:14,440] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:14,441] [INFO] Task started: HMMsearch
[2024-01-24 11:52:14,441] [INFO] Running command: hmmsearch --tblout GCF_019355395.1_ASM1935539v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference/reference_markers.hmm GCF_019355395.1_ASM1935539v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:14,693] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:14,695] [INFO] Found 6/6 markers.
[2024-01-24 11:52:14,722] [INFO] Query marker FASTA was written to GCF_019355395.1_ASM1935539v1_genomic.fna/markers.fasta
[2024-01-24 11:52:14,723] [INFO] Task started: Blastn
[2024-01-24 11:52:14,723] [INFO] Running command: blastn -query GCF_019355395.1_ASM1935539v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference/reference_markers.fasta -out GCF_019355395.1_ASM1935539v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:15,406] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:15,413] [INFO] Selected 30 target genomes.
[2024-01-24 11:52:15,414] [INFO] Target genome list was writen to GCF_019355395.1_ASM1935539v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:15,510] [INFO] Task started: fastANI
[2024-01-24 11:52:15,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d4e74a1-3a9e-4c78-8903-5b8a8a655273/GCF_019355395.1_ASM1935539v1_genomic.fna.gz --refList GCF_019355395.1_ASM1935539v1_genomic.fna/target_genomes.txt --output GCF_019355395.1_ASM1935539v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:35,608] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:35,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:35,618] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:35,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:35,618] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	79.0326	87	1089	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.9291	58	1089	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.4652	53	1089	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.4421	54	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:35,619] [INFO] DFAST Taxonomy check result was written to GCF_019355395.1_ASM1935539v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:35,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:35,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:35,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference/checkm_data
[2024-01-24 11:52:35,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:35,653] [INFO] Task started: CheckM
[2024-01-24 11:52:35,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019355395.1_ASM1935539v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019355395.1_ASM1935539v1_genomic.fna/checkm_input GCF_019355395.1_ASM1935539v1_genomic.fna/checkm_result
[2024-01-24 11:53:05,760] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:05,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:05,784] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:05,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:05,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019355395.1_ASM1935539v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:05,785] [INFO] Task started: Blastn
[2024-01-24 11:53:05,785] [INFO] Running command: blastn -query GCF_019355395.1_ASM1935539v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e48981f-9640-4d0b-8a50-0c171dfe2cb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019355395.1_ASM1935539v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:07,014] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:07,019] [INFO] Selected 23 target genomes.
[2024-01-24 11:53:07,019] [INFO] Target genome list was writen to GCF_019355395.1_ASM1935539v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:07,064] [INFO] Task started: fastANI
[2024-01-24 11:53:07,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d4e74a1-3a9e-4c78-8903-5b8a8a655273/GCF_019355395.1_ASM1935539v1_genomic.fna.gz --refList GCF_019355395.1_ASM1935539v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019355395.1_ASM1935539v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:16,178] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:16,192] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:16,193] [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_900317045.1	s__UBA1066 sp900317045	99.1249	681	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.33	98.92	0.88	0.76	8	conclusive
GCA_900315305.1	s__UBA1066 sp900315305	77.5972	168	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	-
GCA_002350625.1	s__UBA1066 sp002350625	77.4854	158	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.93	99.93	0.93	0.93	2	-
GCA_902766945.1	s__UBA1066 sp902766945	77.4765	124	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320575.1	s__UBA1066 sp900320575	77.2927	104	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.66	99.66	0.99	0.99	2	-
GCA_902766955.1	s__UBA1066 sp902766955	77.1883	121	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	97.96	97.96	0.75	0.75	2	-
GCA_902803245.1	s__UBA1066 sp902803245	76.9218	100	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.12	98.12	0.73	0.73	2	-
GCA_902773195.1	s__UBA1066 sp902773195	76.886	168	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783935.1	s__UBA1066 sp902783935	76.8646	63	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369495.1	s__UBA1066 sp002369495	76.5836	78	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.09	98.09	0.78	0.78	2	-
GCA_017430765.1	s__UBA1066 sp017430765	76.5509	76	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797025.1	s__Bilifractor sp902797025	75.8244	56	1089	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:16,194] [INFO] GTDB search result was written to GCF_019355395.1_ASM1935539v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:16,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:16,199] [INFO] DFAST_QC result json was written to GCF_019355395.1_ASM1935539v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:16,199] [INFO] DFAST_QC completed!
[2024-01-24 11:53:16,199] [INFO] Total running time: 0h1m11s