[2023-07-01 03:31:32,641] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:31:32,643] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:31:32,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference
[2023-07-01 03:31:35,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:31:35,196] [INFO] Task started: Prodigal
[2023-07-01 03:31:35,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgafd3eaf0-f1f4-48ef-9967-eb39dd81b05a/GCA_016287455.1_ASM1628745v1_genomic.fna.gz | prodigal -d GCA_016287455.1_ASM1628745v1_genomic.fna/cds.fna -a GCA_016287455.1_ASM1628745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:31:39,972] [INFO] Task succeeded: Prodigal
[2023-07-01 03:31:39,972] [INFO] Task started: HMMsearch
[2023-07-01 03:31:39,972] [INFO] Running command: hmmsearch --tblout GCA_016287455.1_ASM1628745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference/reference_markers.hmm GCA_016287455.1_ASM1628745v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:31:40,219] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:31:40,220] [INFO] Found 6/6 markers.
[2023-07-01 03:31:40,245] [INFO] Query marker FASTA was written to GCA_016287455.1_ASM1628745v1_genomic.fna/markers.fasta
[2023-07-01 03:31:40,245] [INFO] Task started: Blastn
[2023-07-01 03:31:40,246] [INFO] Running command: blastn -query GCA_016287455.1_ASM1628745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference/reference_markers.fasta -out GCA_016287455.1_ASM1628745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:31:40,827] [INFO] Task succeeded: Blastn
[2023-07-01 03:31:40,832] [INFO] Selected 36 target genomes.
[2023-07-01 03:31:40,832] [INFO] Target genome list was writen to GCA_016287455.1_ASM1628745v1_genomic.fna/target_genomes.txt
[2023-07-01 03:31:40,839] [INFO] Task started: fastANI
[2023-07-01 03:31:40,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgafd3eaf0-f1f4-48ef-9967-eb39dd81b05a/GCA_016287455.1_ASM1628745v1_genomic.fna.gz --refList GCA_016287455.1_ASM1628745v1_genomic.fna/target_genomes.txt --output GCA_016287455.1_ASM1628745v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:32:05,008] [INFO] Task succeeded: fastANI
[2023-07-01 03:32:05,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:32:05,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:32:05,011] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:32:05,012] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 03:32:05,012] [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
--------------------------------------------------------------------------------
[2023-07-01 03:32:05,014] [INFO] DFAST Taxonomy check result was written to GCA_016287455.1_ASM1628745v1_genomic.fna/tc_result.tsv
[2023-07-01 03:32:05,015] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:32:05,015] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:32:05,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference/checkm_data
[2023-07-01 03:32:05,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:32:05,053] [INFO] Task started: CheckM
[2023-07-01 03:32:05,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016287455.1_ASM1628745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016287455.1_ASM1628745v1_genomic.fna/checkm_input GCA_016287455.1_ASM1628745v1_genomic.fna/checkm_result
[2023-07-01 03:32:26,625] [INFO] Task succeeded: CheckM
[2023-07-01 03:32:26,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 19.27%
Strain heterogeneity: 27.27%
--------------------------------------------------------------------------------
[2023-07-01 03:32:26,654] [INFO] ===== Completeness check finished =====
[2023-07-01 03:32:26,656] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:32:26,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016287455.1_ASM1628745v1_genomic.fna/markers.fasta)
[2023-07-01 03:32:26,658] [INFO] Task started: Blastn
[2023-07-01 03:32:26,658] [INFO] Running command: blastn -query GCA_016287455.1_ASM1628745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg556cf89d-ab30-4070-9df0-99da77db6814/dqc_reference/reference_markers_gtdb.fasta -out GCA_016287455.1_ASM1628745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:32:27,500] [INFO] Task succeeded: Blastn
[2023-07-01 03:32:27,505] [INFO] Selected 10 target genomes.
[2023-07-01 03:32:27,505] [INFO] Target genome list was writen to GCA_016287455.1_ASM1628745v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:32:27,511] [INFO] Task started: fastANI
[2023-07-01 03:32:27,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgafd3eaf0-f1f4-48ef-9967-eb39dd81b05a/GCA_016287455.1_ASM1628745v1_genomic.fna.gz --refList GCA_016287455.1_ASM1628745v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016287455.1_ASM1628745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:32:31,564] [INFO] Task succeeded: fastANI
[2023-07-01 03:32:31,574] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:32:31,575] [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_002392505.1	s__UBA3857 sp002392505	97.7929	364	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	97.88	97.88	0.81	0.81	2	conclusive
GCA_017394835.1	s__UBA3857 sp017394835	82.7043	294	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	98.17	98.02	0.93	0.92	4	-
GCA_017619735.1	s__UBA3857 sp017619735	81.0456	293	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541305.1	s__UBA3857 sp017541305	80.8122	282	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	98.04	98.04	0.86	0.86	2	-
GCA_017509785.1	s__UBA3857 sp017509785	80.6959	274	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017616435.1	s__UBA3857 sp017616435	80.385	268	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017614315.1	s__UBA3857 sp017614315	80.2435	211	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539215.1	s__UBA3857 sp017539215	79.2534	176	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3857	95.0	97.97	97.92	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2023-07-01 03:32:31,577] [INFO] GTDB search result was written to GCA_016287455.1_ASM1628745v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:32:31,578] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:32:31,581] [INFO] DFAST_QC result json was written to GCA_016287455.1_ASM1628745v1_genomic.fna/dqc_result.json
[2023-07-01 03:32:31,582] [INFO] DFAST_QC completed!
[2023-07-01 03:32:31,582] [INFO] Total running time: 0h0m59s