[2023-06-30 04:36:31,528] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:36:31,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:36:31,530] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference
[2023-06-30 04:36:33,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:36:33,576] [INFO] Task started: Prodigal
[2023-06-30 04:36:33,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg90e2a1ab-dc06-4aab-9732-5f4b1f7c5552/GCA_007130045.1_ASM713004v1_genomic.fna.gz | prodigal -d GCA_007130045.1_ASM713004v1_genomic.fna/cds.fna -a GCA_007130045.1_ASM713004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:36:52,246] [INFO] Task succeeded: Prodigal
[2023-06-30 04:36:52,247] [INFO] Task started: HMMsearch
[2023-06-30 04:36:52,247] [INFO] Running command: hmmsearch --tblout GCA_007130045.1_ASM713004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference/reference_markers.hmm GCA_007130045.1_ASM713004v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:36:52,484] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:36:52,486] [INFO] Found 6/6 markers.
[2023-06-30 04:36:52,526] [INFO] Query marker FASTA was written to GCA_007130045.1_ASM713004v1_genomic.fna/markers.fasta
[2023-06-30 04:36:52,527] [INFO] Task started: Blastn
[2023-06-30 04:36:52,527] [INFO] Running command: blastn -query GCA_007130045.1_ASM713004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference/reference_markers.fasta -out GCA_007130045.1_ASM713004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:36:53,139] [INFO] Task succeeded: Blastn
[2023-06-30 04:36:53,143] [INFO] Selected 22 target genomes.
[2023-06-30 04:36:53,144] [INFO] Target genome list was writen to GCA_007130045.1_ASM713004v1_genomic.fna/target_genomes.txt
[2023-06-30 04:36:53,148] [INFO] Task started: fastANI
[2023-06-30 04:36:53,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e2a1ab-dc06-4aab-9732-5f4b1f7c5552/GCA_007130045.1_ASM713004v1_genomic.fna.gz --refList GCA_007130045.1_ASM713004v1_genomic.fna/target_genomes.txt --output GCA_007130045.1_ASM713004v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:37:10,097] [INFO] Task succeeded: fastANI
[2023-06-30 04:37:10,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:37:10,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:37:10,100] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:37:10,100] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:37:10,100] [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
--------------------------------------------------------------------------------
[2023-06-30 04:37:10,103] [INFO] DFAST Taxonomy check result was written to GCA_007130045.1_ASM713004v1_genomic.fna/tc_result.tsv
[2023-06-30 04:37:10,103] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:37:10,103] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:37:10,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference/checkm_data
[2023-06-30 04:37:10,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:37:10,144] [INFO] Task started: CheckM
[2023-06-30 04:37:10,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007130045.1_ASM713004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007130045.1_ASM713004v1_genomic.fna/checkm_input GCA_007130045.1_ASM713004v1_genomic.fna/checkm_result
[2023-06-30 04:38:03,642] [INFO] Task succeeded: CheckM
[2023-06-30 04:38:03,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:38:03,666] [INFO] ===== Completeness check finished =====
[2023-06-30 04:38:03,666] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:38:03,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007130045.1_ASM713004v1_genomic.fna/markers.fasta)
[2023-06-30 04:38:03,666] [INFO] Task started: Blastn
[2023-06-30 04:38:03,667] [INFO] Running command: blastn -query GCA_007130045.1_ASM713004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc4c44b4-999a-4fe3-83c9-665a31a032ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_007130045.1_ASM713004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:38:04,538] [INFO] Task succeeded: Blastn
[2023-06-30 04:38:04,543] [INFO] Selected 18 target genomes.
[2023-06-30 04:38:04,543] [INFO] Target genome list was writen to GCA_007130045.1_ASM713004v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:38:04,553] [INFO] Task started: fastANI
[2023-06-30 04:38:04,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg90e2a1ab-dc06-4aab-9732-5f4b1f7c5552/GCA_007130045.1_ASM713004v1_genomic.fna.gz --refList GCA_007130045.1_ASM713004v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007130045.1_ASM713004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:38:15,842] [INFO] Task succeeded: fastANI
[2023-06-30 04:38:15,853] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:38:15,853] [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_007130045.1	s__PXDC01 sp007130045	100.0	1058	1063	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__T3Sed10-336;g__PXDC01	95.0	99.86	99.79	0.94	0.93	4	conclusive
GCA_007132315.1	s__SLOW01 sp007132315	78.0261	171	1063	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__T3Sed10-336;g__SLOW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003558065.1	s__PXDC01 sp003558065	77.9026	248	1063	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__T3Sed10-336;g__PXDC01	95.0	99.75	99.74	0.91	0.90	4	-
GCA_003566885.1	s__SLOW01 sp003566885	77.3355	114	1063	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__T3Sed10-336;g__SLOW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565135.1	s__PXDC01 sp003565135	76.9051	167	1063	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__T3Sed10-336;g__PXDC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695295.1	s__REEB01 sp007695295	75.7105	53	1063	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__REEB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:38:15,855] [INFO] GTDB search result was written to GCA_007130045.1_ASM713004v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:38:15,855] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:38:15,858] [INFO] DFAST_QC result json was written to GCA_007130045.1_ASM713004v1_genomic.fna/dqc_result.json
[2023-06-30 04:38:15,858] [INFO] DFAST_QC completed!
[2023-06-30 04:38:15,858] [INFO] Total running time: 0h1m44s