[2023-06-27 21:27:48,936] [INFO] DFAST_QC pipeline started.
[2023-06-27 21:27:48,938] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 21:27:48,938] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference
[2023-06-27 21:27:50,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 21:27:50,203] [INFO] Task started: Prodigal
[2023-06-27 21:27:50,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d18def2-1a7c-49e8-925a-fe4a8cb3c707/GCA_026708725.1_ASM2670872v1_genomic.fna.gz | prodigal -d GCA_026708725.1_ASM2670872v1_genomic.fna/cds.fna -a GCA_026708725.1_ASM2670872v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 21:27:54,887] [INFO] Task succeeded: Prodigal
[2023-06-27 21:27:54,888] [INFO] Task started: HMMsearch
[2023-06-27 21:27:54,888] [INFO] Running command: hmmsearch --tblout GCA_026708725.1_ASM2670872v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference/reference_markers.hmm GCA_026708725.1_ASM2670872v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 21:27:55,096] [INFO] Task succeeded: HMMsearch
[2023-06-27 21:27:55,097] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9d18def2-1a7c-49e8-925a-fe4a8cb3c707/GCA_026708725.1_ASM2670872v1_genomic.fna.gz]
[2023-06-27 21:27:55,117] [INFO] Query marker FASTA was written to GCA_026708725.1_ASM2670872v1_genomic.fna/markers.fasta
[2023-06-27 21:27:55,118] [INFO] Task started: Blastn
[2023-06-27 21:27:55,118] [INFO] Running command: blastn -query GCA_026708725.1_ASM2670872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference/reference_markers.fasta -out GCA_026708725.1_ASM2670872v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 21:27:55,717] [INFO] Task succeeded: Blastn
[2023-06-27 21:27:55,721] [INFO] Selected 13 target genomes.
[2023-06-27 21:27:55,721] [INFO] Target genome list was writen to GCA_026708725.1_ASM2670872v1_genomic.fna/target_genomes.txt
[2023-06-27 21:27:55,724] [INFO] Task started: fastANI
[2023-06-27 21:27:55,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d18def2-1a7c-49e8-925a-fe4a8cb3c707/GCA_026708725.1_ASM2670872v1_genomic.fna.gz --refList GCA_026708725.1_ASM2670872v1_genomic.fna/target_genomes.txt --output GCA_026708725.1_ASM2670872v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 21:28:05,059] [INFO] Task succeeded: fastANI
[2023-06-27 21:28:05,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 21:28:05,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 21:28:05,065] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 21:28:05,065] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 21:28:05,065] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.0673	66	335	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9101	51	335	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 21:28:05,068] [INFO] DFAST Taxonomy check result was written to GCA_026708725.1_ASM2670872v1_genomic.fna/tc_result.tsv
[2023-06-27 21:28:05,068] [INFO] ===== Taxonomy check completed =====
[2023-06-27 21:28:05,068] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 21:28:05,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference/checkm_data
[2023-06-27 21:28:05,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 21:28:05,092] [INFO] Task started: CheckM
[2023-06-27 21:28:05,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708725.1_ASM2670872v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708725.1_ASM2670872v1_genomic.fna/checkm_input GCA_026708725.1_ASM2670872v1_genomic.fna/checkm_result
[2023-06-27 21:28:25,393] [INFO] Task succeeded: CheckM
[2023-06-27 21:28:25,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 21:28:25,415] [INFO] ===== Completeness check finished =====
[2023-06-27 21:28:25,416] [INFO] ===== Start GTDB Search =====
[2023-06-27 21:28:25,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708725.1_ASM2670872v1_genomic.fna/markers.fasta)
[2023-06-27 21:28:25,416] [INFO] Task started: Blastn
[2023-06-27 21:28:25,417] [INFO] Running command: blastn -query GCA_026708725.1_ASM2670872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda4c9b6-e213-4aa4-bf3e-229453ee4b82/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708725.1_ASM2670872v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 21:28:26,225] [INFO] Task succeeded: Blastn
[2023-06-27 21:28:26,229] [INFO] Selected 12 target genomes.
[2023-06-27 21:28:26,229] [INFO] Target genome list was writen to GCA_026708725.1_ASM2670872v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 21:28:26,232] [INFO] Task started: fastANI
[2023-06-27 21:28:26,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d18def2-1a7c-49e8-925a-fe4a8cb3c707/GCA_026708725.1_ASM2670872v1_genomic.fna.gz --refList GCA_026708725.1_ASM2670872v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708725.1_ASM2670872v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 21:28:32,670] [INFO] Task succeeded: fastANI
[2023-06-27 21:28:32,676] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 21:28:32,677] [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_009842675.1	s__Bin134 sp009842675	83.6549	250	335	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	96.86	96.18	0.91	0.88	13	-
GCA_002239105.1	s__Bin134 sp002239105	82.6561	258	335	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843565.1	s__Bin134 sp009843565	81.8745	171	335	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__Bin134	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	77.1486	54	335	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	76.5069	78	335	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.2704	58	335	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 21:28:32,679] [INFO] GTDB search result was written to GCA_026708725.1_ASM2670872v1_genomic.fna/result_gtdb.tsv
[2023-06-27 21:28:32,679] [INFO] ===== GTDB Search completed =====
[2023-06-27 21:28:32,682] [INFO] DFAST_QC result json was written to GCA_026708725.1_ASM2670872v1_genomic.fna/dqc_result.json
[2023-06-27 21:28:32,682] [INFO] DFAST_QC completed!
[2023-06-27 21:28:32,682] [INFO] Total running time: 0h0m44s