[2023-06-13 07:44:10,016] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:44:10,019] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:44:10,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference
[2023-06-13 07:44:11,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:44:11,223] [INFO] Task started: Prodigal
[2023-06-13 07:44:11,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg61897abe-8d8a-4c8d-a692-6a13d74a4be6/GCA_022484165.1_ASM2248416v1_genomic.fna.gz | prodigal -d GCA_022484165.1_ASM2248416v1_genomic.fna/cds.fna -a GCA_022484165.1_ASM2248416v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:44:18,495] [INFO] Task succeeded: Prodigal
[2023-06-13 07:44:18,496] [INFO] Task started: HMMsearch
[2023-06-13 07:44:18,496] [INFO] Running command: hmmsearch --tblout GCA_022484165.1_ASM2248416v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference/reference_markers.hmm GCA_022484165.1_ASM2248416v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:44:18,744] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:44:18,746] [INFO] Found 6/6 markers.
[2023-06-13 07:44:18,772] [INFO] Query marker FASTA was written to GCA_022484165.1_ASM2248416v1_genomic.fna/markers.fasta
[2023-06-13 07:44:18,772] [INFO] Task started: Blastn
[2023-06-13 07:44:18,772] [INFO] Running command: blastn -query GCA_022484165.1_ASM2248416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference/reference_markers.fasta -out GCA_022484165.1_ASM2248416v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:44:19,442] [INFO] Task succeeded: Blastn
[2023-06-13 07:44:19,447] [INFO] Selected 34 target genomes.
[2023-06-13 07:44:19,448] [INFO] Target genome list was writen to GCA_022484165.1_ASM2248416v1_genomic.fna/target_genomes.txt
[2023-06-13 07:44:19,455] [INFO] Task started: fastANI
[2023-06-13 07:44:19,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg61897abe-8d8a-4c8d-a692-6a13d74a4be6/GCA_022484165.1_ASM2248416v1_genomic.fna.gz --refList GCA_022484165.1_ASM2248416v1_genomic.fna/target_genomes.txt --output GCA_022484165.1_ASM2248416v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:44:38,125] [INFO] Task succeeded: fastANI
[2023-06-13 07:44:38,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:44:38,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:44:38,133] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 07:44:38,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 07:44:38,134] [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
Porcincola intestinalis	strain=Oil+RF-744-WCA-WT-11	GCA_009696445.1	2606632	2606632	type	True	77.9285	55	904	95	below_threshold
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	77.5264	64	904	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 07:44:38,136] [INFO] DFAST Taxonomy check result was written to GCA_022484165.1_ASM2248416v1_genomic.fna/tc_result.tsv
[2023-06-13 07:44:38,137] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:44:38,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:44:38,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference/checkm_data
[2023-06-13 07:44:38,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:44:38,169] [INFO] Task started: CheckM
[2023-06-13 07:44:38,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022484165.1_ASM2248416v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022484165.1_ASM2248416v1_genomic.fna/checkm_input GCA_022484165.1_ASM2248416v1_genomic.fna/checkm_result
[2023-06-13 07:45:05,539] [INFO] Task succeeded: CheckM
[2023-06-13 07:45:05,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:45:05,568] [INFO] ===== Completeness check finished =====
[2023-06-13 07:45:05,568] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:45:05,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022484165.1_ASM2248416v1_genomic.fna/markers.fasta)
[2023-06-13 07:45:05,569] [INFO] Task started: Blastn
[2023-06-13 07:45:05,569] [INFO] Running command: blastn -query GCA_022484165.1_ASM2248416v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8be22c9d-28a6-4f7f-bed8-1e19e82d33d8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022484165.1_ASM2248416v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:45:06,706] [INFO] Task succeeded: Blastn
[2023-06-13 07:45:06,711] [INFO] Selected 16 target genomes.
[2023-06-13 07:45:06,711] [INFO] Target genome list was writen to GCA_022484165.1_ASM2248416v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:45:06,722] [INFO] Task started: fastANI
[2023-06-13 07:45:06,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg61897abe-8d8a-4c8d-a692-6a13d74a4be6/GCA_022484165.1_ASM2248416v1_genomic.fna.gz --refList GCA_022484165.1_ASM2248416v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022484165.1_ASM2248416v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:45:13,823] [INFO] Task succeeded: fastANI
[2023-06-13 07:45:13,836] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 07:45:13,836] [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_900315305.1	s__UBA1066 sp900315305	98.4304	654	904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.26	98.90	0.90	0.82	11	conclusive
GCA_900320615.1	s__UBA1066 sp900320615	88.7806	500	904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.42	99.12	0.88	0.79	4	-
GCA_900317045.1	s__UBA1066 sp900317045	77.7274	144	904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	99.33	98.92	0.88	0.76	8	-
GCA_900317515.1	s__UBA1066 sp900317515	77.4314	118	904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.06	96.06	0.86	0.79	9	-
GCA_002350625.1	s__UBA1066 sp002350625	77.2932	121	904	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_902773195.1	s__UBA1066 sp902773195	77.165	89	904	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_900314565.1	s__UBA1066 sp900314565	77.1245	101	904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	98.26	96.12	0.90	0.66	19	-
GCA_902766945.1	s__UBA1066 sp902766945	76.9693	96	904	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_902766955.1	s__UBA1066 sp902766955	76.9095	97	904	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_002371465.1	s__UBA1066 sp002371465	76.8701	95	904	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_902803505.1	s__UBA1066 sp902803505	76.7298	62	904	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	76.4483	93	904	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_902783325.1	s__UBA1066 sp902783325	76.368	87	904	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1066	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 07:45:13,838] [INFO] GTDB search result was written to GCA_022484165.1_ASM2248416v1_genomic.fna/result_gtdb.tsv
[2023-06-13 07:45:13,839] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:45:13,842] [INFO] DFAST_QC result json was written to GCA_022484165.1_ASM2248416v1_genomic.fna/dqc_result.json
[2023-06-13 07:45:13,842] [INFO] DFAST_QC completed!
[2023-06-13 07:45:13,842] [INFO] Total running time: 0h1m4s