[2023-06-05 15:05:44,017] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:05:44,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:05:44,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference
[2023-06-05 15:05:45,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:05:45,284] [INFO] Task started: Prodigal
[2023-06-05 15:05:45,284] [INFO] Running command: gunzip -c /var/lib/cwl/stge5e85945-b724-4ece-b1b6-5988f930b6a3/GCA_004554005.1_ASM455400v1_genomic.fna.gz | prodigal -d GCA_004554005.1_ASM455400v1_genomic.fna/cds.fna -a GCA_004554005.1_ASM455400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:05:48,867] [INFO] Task succeeded: Prodigal
[2023-06-05 15:05:48,868] [INFO] Task started: HMMsearch
[2023-06-05 15:05:48,868] [INFO] Running command: hmmsearch --tblout GCA_004554005.1_ASM455400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference/reference_markers.hmm GCA_004554005.1_ASM455400v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:05:49,061] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:05:49,062] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5e85945-b724-4ece-b1b6-5988f930b6a3/GCA_004554005.1_ASM455400v1_genomic.fna.gz]
[2023-06-05 15:05:49,081] [INFO] Query marker FASTA was written to GCA_004554005.1_ASM455400v1_genomic.fna/markers.fasta
[2023-06-05 15:05:49,082] [INFO] Task started: Blastn
[2023-06-05 15:05:49,082] [INFO] Running command: blastn -query GCA_004554005.1_ASM455400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference/reference_markers.fasta -out GCA_004554005.1_ASM455400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:49,711] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:49,715] [INFO] Selected 27 target genomes.
[2023-06-05 15:05:49,716] [INFO] Target genome list was writen to GCA_004554005.1_ASM455400v1_genomic.fna/target_genomes.txt
[2023-06-05 15:05:49,722] [INFO] Task started: fastANI
[2023-06-05 15:05:49,723] [INFO] Running command: fastANI --query /var/lib/cwl/stge5e85945-b724-4ece-b1b6-5988f930b6a3/GCA_004554005.1_ASM455400v1_genomic.fna.gz --refList GCA_004554005.1_ASM455400v1_genomic.fna/target_genomes.txt --output GCA_004554005.1_ASM455400v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:06:02,893] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:02,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:06:02,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:06:02,897] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:06:02,897] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 15:06:02,897] [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
--------------------------------------------------------------------------------
[2023-06-05 15:06:02,899] [INFO] DFAST Taxonomy check result was written to GCA_004554005.1_ASM455400v1_genomic.fna/tc_result.tsv
[2023-06-05 15:06:02,900] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:06:02,900] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:06:02,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference/checkm_data
[2023-06-05 15:06:02,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:06:02,925] [INFO] Task started: CheckM
[2023-06-05 15:06:02,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004554005.1_ASM455400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004554005.1_ASM455400v1_genomic.fna/checkm_input GCA_004554005.1_ASM455400v1_genomic.fna/checkm_result
[2023-06-05 15:06:24,509] [INFO] Task succeeded: CheckM
[2023-06-05 15:06:24,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 15:06:24,664] [INFO] ===== Completeness check finished =====
[2023-06-05 15:06:24,664] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:06:24,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004554005.1_ASM455400v1_genomic.fna/markers.fasta)
[2023-06-05 15:06:24,665] [INFO] Task started: Blastn
[2023-06-05 15:06:24,665] [INFO] Running command: blastn -query GCA_004554005.1_ASM455400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c6a0af4-46dc-438b-8ff2-39a9d964049c/dqc_reference/reference_markers_gtdb.fasta -out GCA_004554005.1_ASM455400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:06:25,817] [INFO] Task succeeded: Blastn
[2023-06-05 15:06:25,821] [INFO] Selected 18 target genomes.
[2023-06-05 15:06:25,821] [INFO] Target genome list was writen to GCA_004554005.1_ASM455400v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:06:25,829] [INFO] Task started: fastANI
[2023-06-05 15:06:25,829] [INFO] Running command: fastANI --query /var/lib/cwl/stge5e85945-b724-4ece-b1b6-5988f930b6a3/GCA_004554005.1_ASM455400v1_genomic.fna.gz --refList GCA_004554005.1_ASM455400v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004554005.1_ASM455400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:06:32,407] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:32,416] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 15:06:32,417] [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_000435055.1	s__PeH17 sp000435055	98.7801	337	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.45	98.03	0.92	0.89	15	conclusive
GCA_902794055.1	s__PeH17 sp902794055	77.8477	57	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017395105.1	s__PeH17 sp017395105	77.7184	55	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542285.1	s__PeH17 sp900542285	77.6365	59	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.90	98.16	0.94	0.91	7	-
GCA_017525875.1	s__PeH17 sp017525875	77.6192	51	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	97.79	97.79	0.91	0.91	2	-
GCA_017523925.1	s__PeH17 sp017523925	77.4119	64	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538255.1	s__PeH17 sp017538255	76.9881	60	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288175.1	s__PeH17 sp016288175	76.9712	56	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.53	98.53	0.71	0.71	2	-
GCA_017553815.1	s__PeH17 sp017553815	76.6563	58	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 15:06:32,419] [INFO] GTDB search result was written to GCA_004554005.1_ASM455400v1_genomic.fna/result_gtdb.tsv
[2023-06-05 15:06:32,419] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:06:32,423] [INFO] DFAST_QC result json was written to GCA_004554005.1_ASM455400v1_genomic.fna/dqc_result.json
[2023-06-05 15:06:32,423] [INFO] DFAST_QC completed!
[2023-06-05 15:06:32,423] [INFO] Total running time: 0h0m48s