[2023-06-18 17:28:40,294] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:28:40,296] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:28:40,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference
[2023-06-18 17:28:41,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:28:41,466] [INFO] Task started: Prodigal
[2023-06-18 17:28:41,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg532556be-d47f-4fdc-8dca-34417767ca05/GCA_013202925.1_ASM1320292v1_genomic.fna.gz | prodigal -d GCA_013202925.1_ASM1320292v1_genomic.fna/cds.fna -a GCA_013202925.1_ASM1320292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:28:43,830] [INFO] Task succeeded: Prodigal
[2023-06-18 17:28:43,831] [INFO] Task started: HMMsearch
[2023-06-18 17:28:43,831] [INFO] Running command: hmmsearch --tblout GCA_013202925.1_ASM1320292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference/reference_markers.hmm GCA_013202925.1_ASM1320292v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:28:44,062] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:28:44,064] [INFO] Found 6/6 markers.
[2023-06-18 17:28:44,084] [INFO] Query marker FASTA was written to GCA_013202925.1_ASM1320292v1_genomic.fna/markers.fasta
[2023-06-18 17:28:44,084] [INFO] Task started: Blastn
[2023-06-18 17:28:44,084] [INFO] Running command: blastn -query GCA_013202925.1_ASM1320292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference/reference_markers.fasta -out GCA_013202925.1_ASM1320292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:28:44,682] [INFO] Task succeeded: Blastn
[2023-06-18 17:28:44,693] [INFO] Selected 11 target genomes.
[2023-06-18 17:28:44,694] [INFO] Target genome list was writen to GCA_013202925.1_ASM1320292v1_genomic.fna/target_genomes.txt
[2023-06-18 17:28:44,698] [INFO] Task started: fastANI
[2023-06-18 17:28:44,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg532556be-d47f-4fdc-8dca-34417767ca05/GCA_013202925.1_ASM1320292v1_genomic.fna.gz --refList GCA_013202925.1_ASM1320292v1_genomic.fna/target_genomes.txt --output GCA_013202925.1_ASM1320292v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:28:50,541] [INFO] Task succeeded: fastANI
[2023-06-18 17:28:50,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:28:50,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:28:50,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:28:50,544] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:28:50,544] [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
--------------------------------------------------------------------------------
[2023-06-18 17:28:50,545] [INFO] DFAST Taxonomy check result was written to GCA_013202925.1_ASM1320292v1_genomic.fna/tc_result.tsv
[2023-06-18 17:28:50,548] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:28:50,548] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:28:50,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference/checkm_data
[2023-06-18 17:28:50,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:28:50,571] [INFO] Task started: CheckM
[2023-06-18 17:28:50,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013202925.1_ASM1320292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013202925.1_ASM1320292v1_genomic.fna/checkm_input GCA_013202925.1_ASM1320292v1_genomic.fna/checkm_result
[2023-06-18 17:29:06,208] [INFO] Task succeeded: CheckM
[2023-06-18 17:29:06,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-18 17:29:06,243] [INFO] ===== Completeness check finished =====
[2023-06-18 17:29:06,244] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:29:06,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013202925.1_ASM1320292v1_genomic.fna/markers.fasta)
[2023-06-18 17:29:06,244] [INFO] Task started: Blastn
[2023-06-18 17:29:06,245] [INFO] Running command: blastn -query GCA_013202925.1_ASM1320292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg828003d3-d105-4e88-9a02-0b541329fdfd/dqc_reference/reference_markers_gtdb.fasta -out GCA_013202925.1_ASM1320292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:29:07,050] [INFO] Task succeeded: Blastn
[2023-06-18 17:29:07,055] [INFO] Selected 15 target genomes.
[2023-06-18 17:29:07,055] [INFO] Target genome list was writen to GCA_013202925.1_ASM1320292v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:29:07,089] [INFO] Task started: fastANI
[2023-06-18 17:29:07,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg532556be-d47f-4fdc-8dca-34417767ca05/GCA_013202925.1_ASM1320292v1_genomic.fna.gz --refList GCA_013202925.1_ASM1320292v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013202925.1_ASM1320292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:29:11,248] [INFO] Task succeeded: fastANI
[2023-06-18 17:29:11,258] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:29:11,258] [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_013202925.1	s__JABMRA01 sp013202925	99.9999	300	304	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JABMRA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018902915.1	s__JAHIPS01 sp018902915	78.801	116	304	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHIPS01	95.0	99.40	99.40	0.74	0.74	2	-
GCA_018896815.1	s__JAHILY01 sp018896815	78.1482	80	304	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHILY01	95.0	99.67	99.67	0.84	0.84	2	-
GCA_018901615.1	s__JAHIEN01 sp018901615	77.7158	68	304	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHIEN01	95.0	99.28	99.28	0.87	0.87	2	-
GCA_018818505.1	s__JAHIRR01 sp018818505	76.7527	62	304	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHIRR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:29:11,260] [INFO] GTDB search result was written to GCA_013202925.1_ASM1320292v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:29:11,265] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:29:11,267] [INFO] DFAST_QC result json was written to GCA_013202925.1_ASM1320292v1_genomic.fna/dqc_result.json
[2023-06-18 17:29:11,268] [INFO] DFAST_QC completed!
[2023-06-18 17:29:11,268] [INFO] Total running time: 0h0m31s