[2023-06-29 04:41:50,168] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:50,170] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:50,170] [INFO] DQC Reference Directory: /var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference
[2023-06-29 04:41:51,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:51,406] [INFO] Task started: Prodigal
[2023-06-29 04:41:51,407] [INFO] Running command: gunzip -c /var/lib/cwl/stg54014e1e-8a90-40e8-b54e-66c22e3a6f73/GCA_020626545.1_ASM2062654v1_genomic.fna.gz | prodigal -d GCA_020626545.1_ASM2062654v1_genomic.fna/cds.fna -a GCA_020626545.1_ASM2062654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:54,131] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:54,132] [INFO] Task started: HMMsearch
[2023-06-29 04:41:54,132] [INFO] Running command: hmmsearch --tblout GCA_020626545.1_ASM2062654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference/reference_markers.hmm GCA_020626545.1_ASM2062654v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:41:54,371] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:41:54,373] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg54014e1e-8a90-40e8-b54e-66c22e3a6f73/GCA_020626545.1_ASM2062654v1_genomic.fna.gz]
[2023-06-29 04:41:54,394] [INFO] Query marker FASTA was written to GCA_020626545.1_ASM2062654v1_genomic.fna/markers.fasta
[2023-06-29 04:41:54,395] [INFO] Task started: Blastn
[2023-06-29 04:41:54,395] [INFO] Running command: blastn -query GCA_020626545.1_ASM2062654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference/reference_markers.fasta -out GCA_020626545.1_ASM2062654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:41:55,026] [INFO] Task succeeded: Blastn
[2023-06-29 04:41:55,031] [INFO] Selected 17 target genomes.
[2023-06-29 04:41:55,032] [INFO] Target genome list was writen to GCA_020626545.1_ASM2062654v1_genomic.fna/target_genomes.txt
[2023-06-29 04:41:55,036] [INFO] Task started: fastANI
[2023-06-29 04:41:55,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg54014e1e-8a90-40e8-b54e-66c22e3a6f73/GCA_020626545.1_ASM2062654v1_genomic.fna.gz --refList GCA_020626545.1_ASM2062654v1_genomic.fna/target_genomes.txt --output GCA_020626545.1_ASM2062654v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:42:05,714] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:05,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:42:05,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:42:05,721] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:42:05,722] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:42:05,722] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	76.2691	54	473	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:42:05,724] [INFO] DFAST Taxonomy check result was written to GCA_020626545.1_ASM2062654v1_genomic.fna/tc_result.tsv
[2023-06-29 04:42:05,725] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:42:05,725] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:42:05,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference/checkm_data
[2023-06-29 04:42:05,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:42:05,757] [INFO] Task started: CheckM
[2023-06-29 04:42:05,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020626545.1_ASM2062654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020626545.1_ASM2062654v1_genomic.fna/checkm_input GCA_020626545.1_ASM2062654v1_genomic.fna/checkm_result
[2023-06-29 04:42:22,349] [INFO] Task succeeded: CheckM
[2023-06-29 04:42:22,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.37%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 04:42:22,373] [INFO] ===== Completeness check finished =====
[2023-06-29 04:42:22,374] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:42:22,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020626545.1_ASM2062654v1_genomic.fna/markers.fasta)
[2023-06-29 04:42:22,375] [INFO] Task started: Blastn
[2023-06-29 04:42:22,375] [INFO] Running command: blastn -query GCA_020626545.1_ASM2062654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20b9da34-b2ad-457c-934d-1df5ae169a4a/dqc_reference/reference_markers_gtdb.fasta -out GCA_020626545.1_ASM2062654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:23,310] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:23,315] [INFO] Selected 11 target genomes.
[2023-06-29 04:42:23,315] [INFO] Target genome list was writen to GCA_020626545.1_ASM2062654v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:42:23,321] [INFO] Task started: fastANI
[2023-06-29 04:42:23,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg54014e1e-8a90-40e8-b54e-66c22e3a6f73/GCA_020626545.1_ASM2062654v1_genomic.fna.gz --refList GCA_020626545.1_ASM2062654v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020626545.1_ASM2062654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:42:27,168] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:27,179] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:42:27,180] [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_002350765.1	s__Ruminococcus_E sp002350765	82.1809	326	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.60	96.50	0.89	0.85	6	-
GCA_902793125.1	s__Ruminococcus_E sp902793125	80.9957	265	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797225.1	s__Ruminococcus_E sp902797225	80.4228	265	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.54	98.30	0.88	0.86	3	-
GCA_905234015.1	s__Ruminococcus_E sp905234015	79.8637	256	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234305.1	s__Ruminococcus_E sp905234305	79.8625	191	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797655.1	s__Ruminococcus_E sp902797655	78.3923	163	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.42	98.42	0.89	0.89	2	-
GCA_900315785.1	s__Ruminococcus_E sp900315785	77.9878	140	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.77	99.77	0.94	0.94	2	-
GCA_902773035.1	s__Ruminococcus_E sp902773035	77.6018	136	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316385.1	s__Ruminococcus_E sp900316385	77.4591	130	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-29 04:42:27,182] [INFO] GTDB search result was written to GCA_020626545.1_ASM2062654v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:42:27,182] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:42:27,185] [INFO] DFAST_QC result json was written to GCA_020626545.1_ASM2062654v1_genomic.fna/dqc_result.json
[2023-06-29 04:42:27,185] [INFO] DFAST_QC completed!
[2023-06-29 04:42:27,185] [INFO] Total running time: 0h0m37s