[2023-06-27 10:10:19,411] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:10:19,453] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:10:19,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference
[2023-06-27 10:10:20,669] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:10:20,669] [INFO] Task started: Prodigal
[2023-06-27 10:10:20,669] [INFO] Running command: gunzip -c /var/lib/cwl/stgba960d04-e3bf-48c8-9c1c-af70c90c48c9/GCA_002685605.1_ASM268560v1_genomic.fna.gz | prodigal -d GCA_002685605.1_ASM268560v1_genomic.fna/cds.fna -a GCA_002685605.1_ASM268560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:10:23,990] [INFO] Task succeeded: Prodigal
[2023-06-27 10:10:23,991] [INFO] Task started: HMMsearch
[2023-06-27 10:10:23,991] [INFO] Running command: hmmsearch --tblout GCA_002685605.1_ASM268560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference/reference_markers.hmm GCA_002685605.1_ASM268560v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:10:24,196] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:10:24,197] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba960d04-e3bf-48c8-9c1c-af70c90c48c9/GCA_002685605.1_ASM268560v1_genomic.fna.gz]
[2023-06-27 10:10:24,589] [INFO] Query marker FASTA was written to GCA_002685605.1_ASM268560v1_genomic.fna/markers.fasta
[2023-06-27 10:10:24,590] [INFO] Task started: Blastn
[2023-06-27 10:10:24,590] [INFO] Running command: blastn -query GCA_002685605.1_ASM268560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference/reference_markers.fasta -out GCA_002685605.1_ASM268560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:10:25,122] [INFO] Task succeeded: Blastn
[2023-06-27 10:10:25,147] [INFO] Selected 20 target genomes.
[2023-06-27 10:10:25,147] [INFO] Target genome list was writen to GCA_002685605.1_ASM268560v1_genomic.fna/target_genomes.txt
[2023-06-27 10:10:25,149] [INFO] Task started: fastANI
[2023-06-27 10:10:25,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgba960d04-e3bf-48c8-9c1c-af70c90c48c9/GCA_002685605.1_ASM268560v1_genomic.fna.gz --refList GCA_002685605.1_ASM268560v1_genomic.fna/target_genomes.txt --output GCA_002685605.1_ASM268560v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:10:37,379] [INFO] Task succeeded: fastANI
[2023-06-27 10:10:37,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:10:37,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:10:38,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:10:38,383] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 10:10:38,383] [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
--------------------------------------------------------------------------------
[2023-06-27 10:10:38,385] [INFO] DFAST Taxonomy check result was written to GCA_002685605.1_ASM268560v1_genomic.fna/tc_result.tsv
[2023-06-27 10:10:38,386] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:10:38,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:10:38,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference/checkm_data
[2023-06-27 10:10:38,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:10:38,408] [INFO] Task started: CheckM
[2023-06-27 10:10:38,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002685605.1_ASM268560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002685605.1_ASM268560v1_genomic.fna/checkm_input GCA_002685605.1_ASM268560v1_genomic.fna/checkm_result
[2023-06-27 10:10:56,955] [INFO] Task succeeded: CheckM
[2023-06-27 10:10:56,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 10:10:57,151] [INFO] ===== Completeness check finished =====
[2023-06-27 10:10:57,151] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:10:57,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002685605.1_ASM268560v1_genomic.fna/markers.fasta)
[2023-06-27 10:10:57,151] [INFO] Task started: Blastn
[2023-06-27 10:10:57,151] [INFO] Running command: blastn -query GCA_002685605.1_ASM268560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c3b804a-47cb-4309-981d-326b9dff2513/dqc_reference/reference_markers_gtdb.fasta -out GCA_002685605.1_ASM268560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:10:57,837] [INFO] Task succeeded: Blastn
[2023-06-27 10:10:57,840] [INFO] Selected 12 target genomes.
[2023-06-27 10:10:57,840] [INFO] Target genome list was writen to GCA_002685605.1_ASM268560v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:10:57,883] [INFO] Task started: fastANI
[2023-06-27 10:10:57,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgba960d04-e3bf-48c8-9c1c-af70c90c48c9/GCA_002685605.1_ASM268560v1_genomic.fna.gz --refList GCA_002685605.1_ASM268560v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002685605.1_ASM268560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:11:02,518] [INFO] Task succeeded: fastANI
[2023-06-27 10:11:02,523] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 10:11:02,524] [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_002436185.1	s__UBA2126 sp002436185	99.8281	441	532	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.90	99.88	0.91	0.83	5	conclusive
GCA_002256485.1	s__UBA2126 sp002256485	86.5439	398	532	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381755.1	s__UBA2126 sp014381755	86.3316	356	532	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730315.1	s__UBA2126 sp002730315	82.5787	159	532	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.18	99.07	0.56	0.51	3	-
GCA_002713385.1	s__UBA2126 sp002713385	79.6026	194	532	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	95.44	95.44	0.61	0.61	2	-
GCA_004124385.1	s__UBA2126 sp004124385	79.2047	257	532	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	99.49	99.49	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-27 10:11:02,620] [INFO] GTDB search result was written to GCA_002685605.1_ASM268560v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:11:02,620] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:11:02,623] [INFO] DFAST_QC result json was written to GCA_002685605.1_ASM268560v1_genomic.fna/dqc_result.json
[2023-06-27 10:11:02,623] [INFO] DFAST_QC completed!
[2023-06-27 10:11:02,623] [INFO] Total running time: 0h0m43s