[2023-06-17 07:31:14,634] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:31:14,638] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:31:14,638] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference
[2023-06-17 07:31:15,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:31:15,951] [INFO] Task started: Prodigal
[2023-06-17 07:31:15,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cd00318-764d-40bc-af2b-1b67ecc181b2/GCA_003560065.1_ASM356006v1_genomic.fna.gz | prodigal -d GCA_003560065.1_ASM356006v1_genomic.fna/cds.fna -a GCA_003560065.1_ASM356006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:31:23,062] [INFO] Task succeeded: Prodigal
[2023-06-17 07:31:23,062] [INFO] Task started: HMMsearch
[2023-06-17 07:31:23,062] [INFO] Running command: hmmsearch --tblout GCA_003560065.1_ASM356006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference/reference_markers.hmm GCA_003560065.1_ASM356006v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:31:23,329] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:31:23,330] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2cd00318-764d-40bc-af2b-1b67ecc181b2/GCA_003560065.1_ASM356006v1_genomic.fna.gz]
[2023-06-17 07:31:23,388] [INFO] Query marker FASTA was written to GCA_003560065.1_ASM356006v1_genomic.fna/markers.fasta
[2023-06-17 07:31:23,389] [INFO] Task started: Blastn
[2023-06-17 07:31:23,389] [INFO] Running command: blastn -query GCA_003560065.1_ASM356006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference/reference_markers.fasta -out GCA_003560065.1_ASM356006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:31:24,036] [INFO] Task succeeded: Blastn
[2023-06-17 07:31:24,040] [INFO] Selected 18 target genomes.
[2023-06-17 07:31:24,040] [INFO] Target genome list was writen to GCA_003560065.1_ASM356006v1_genomic.fna/target_genomes.txt
[2023-06-17 07:31:24,042] [INFO] Task started: fastANI
[2023-06-17 07:31:24,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cd00318-764d-40bc-af2b-1b67ecc181b2/GCA_003560065.1_ASM356006v1_genomic.fna.gz --refList GCA_003560065.1_ASM356006v1_genomic.fna/target_genomes.txt --output GCA_003560065.1_ASM356006v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:31:44,844] [INFO] Task succeeded: fastANI
[2023-06-17 07:31:44,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:31:44,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:31:44,848] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:31:44,849] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 07:31:44,849] [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
Dactylosporangium vinaceum	strain=NRRL B-16297	GCA_019904175.1	53362	53362	type	True	74.68	51	817	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:31:44,851] [INFO] DFAST Taxonomy check result was written to GCA_003560065.1_ASM356006v1_genomic.fna/tc_result.tsv
[2023-06-17 07:31:44,852] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:31:44,852] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:31:44,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference/checkm_data
[2023-06-17 07:31:44,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:31:44,889] [INFO] Task started: CheckM
[2023-06-17 07:31:44,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003560065.1_ASM356006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003560065.1_ASM356006v1_genomic.fna/checkm_input GCA_003560065.1_ASM356006v1_genomic.fna/checkm_result
[2023-06-17 07:32:11,590] [INFO] Task succeeded: CheckM
[2023-06-17 07:32:11,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:32:11,613] [INFO] ===== Completeness check finished =====
[2023-06-17 07:32:11,613] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:32:11,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003560065.1_ASM356006v1_genomic.fna/markers.fasta)
[2023-06-17 07:32:11,614] [INFO] Task started: Blastn
[2023-06-17 07:32:11,614] [INFO] Running command: blastn -query GCA_003560065.1_ASM356006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfb4f809-bd9b-4b88-b308-0b058b08cff4/dqc_reference/reference_markers_gtdb.fasta -out GCA_003560065.1_ASM356006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:32:12,583] [INFO] Task succeeded: Blastn
[2023-06-17 07:32:12,587] [INFO] Selected 11 target genomes.
[2023-06-17 07:32:12,587] [INFO] Target genome list was writen to GCA_003560065.1_ASM356006v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:32:12,601] [INFO] Task started: fastANI
[2023-06-17 07:32:12,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cd00318-764d-40bc-af2b-1b67ecc181b2/GCA_003560065.1_ASM356006v1_genomic.fna.gz --refList GCA_003560065.1_ASM356006v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003560065.1_ASM356006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:32:19,464] [INFO] Task succeeded: fastANI
[2023-06-17 07:32:19,480] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:32:19,481] [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_007121555.1	s__PWLA01 sp007121555	99.5294	688	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.62	99.53	0.92	0.84	4	conclusive
GCA_003562075.1	s__PWLA01 sp003562075	78.4608	253	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.40	99.40	0.92	0.92	2	-
GCA_007695195.1	s__PWLA01 sp007695195	78.3801	246	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121775.1	s__PWLA01 sp007121775	78.3493	202	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.55	99.40	0.89	0.80	6	-
GCA_007132965.1	s__PWLA01 sp007132965	78.2179	228	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.78	99.76	0.93	0.93	3	-
GCA_003559555.1	s__PWLA01 sp003559555	78.1678	277	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003567615.1	s__PWLA01 sp003567615	77.9315	148	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129525.1	s__PWLA01 sp007129525	77.6654	156	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	98.95	98.95	0.75	0.75	2	-
GCA_007692505.1	s__REBX01 sp007692505	77.6377	165	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__REBX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126575.1	s__SLBA01 sp007126575	77.2699	172	817	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.74	99.74	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-17 07:32:19,483] [INFO] GTDB search result was written to GCA_003560065.1_ASM356006v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:32:19,483] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:32:19,486] [INFO] DFAST_QC result json was written to GCA_003560065.1_ASM356006v1_genomic.fna/dqc_result.json
[2023-06-17 07:32:19,486] [INFO] DFAST_QC completed!
[2023-06-17 07:32:19,486] [INFO] Total running time: 0h1m5s