[2023-06-28 23:25:39,764] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:25:39,766] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:25:39,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference
[2023-06-28 23:25:41,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:25:41,181] [INFO] Task started: Prodigal
[2023-06-28 23:25:41,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c50395d-6f50-4097-8089-6692a5595325/GCA_020717895.1_ASM2071789v1_genomic.fna.gz | prodigal -d GCA_020717895.1_ASM2071789v1_genomic.fna/cds.fna -a GCA_020717895.1_ASM2071789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:25:54,244] [INFO] Task succeeded: Prodigal
[2023-06-28 23:25:54,245] [INFO] Task started: HMMsearch
[2023-06-28 23:25:54,245] [INFO] Running command: hmmsearch --tblout GCA_020717895.1_ASM2071789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference/reference_markers.hmm GCA_020717895.1_ASM2071789v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:25:54,590] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:25:54,591] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8c50395d-6f50-4097-8089-6692a5595325/GCA_020717895.1_ASM2071789v1_genomic.fna.gz]
[2023-06-28 23:25:54,637] [INFO] Query marker FASTA was written to GCA_020717895.1_ASM2071789v1_genomic.fna/markers.fasta
[2023-06-28 23:25:54,637] [INFO] Task started: Blastn
[2023-06-28 23:25:54,638] [INFO] Running command: blastn -query GCA_020717895.1_ASM2071789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference/reference_markers.fasta -out GCA_020717895.1_ASM2071789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:55,294] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:55,298] [INFO] Selected 19 target genomes.
[2023-06-28 23:25:55,298] [INFO] Target genome list was writen to GCA_020717895.1_ASM2071789v1_genomic.fna/target_genomes.txt
[2023-06-28 23:25:55,301] [INFO] Task started: fastANI
[2023-06-28 23:25:55,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c50395d-6f50-4097-8089-6692a5595325/GCA_020717895.1_ASM2071789v1_genomic.fna.gz --refList GCA_020717895.1_ASM2071789v1_genomic.fna/target_genomes.txt --output GCA_020717895.1_ASM2071789v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:26:08,484] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:08,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:26:08,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:26:08,492] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:26:08,492] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:26:08,493] [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
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.6278	99	1553	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.5848	99	1553	95	below_threshold
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	75.611	78	1553	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:26:08,495] [INFO] DFAST Taxonomy check result was written to GCA_020717895.1_ASM2071789v1_genomic.fna/tc_result.tsv
[2023-06-28 23:26:08,496] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:26:08,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:26:08,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference/checkm_data
[2023-06-28 23:26:08,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:26:08,551] [INFO] Task started: CheckM
[2023-06-28 23:26:08,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020717895.1_ASM2071789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020717895.1_ASM2071789v1_genomic.fna/checkm_input GCA_020717895.1_ASM2071789v1_genomic.fna/checkm_result
[2023-06-28 23:26:50,486] [INFO] Task succeeded: CheckM
[2023-06-28 23:26:50,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.05%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:26:50,513] [INFO] ===== Completeness check finished =====
[2023-06-28 23:26:50,513] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:26:50,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020717895.1_ASM2071789v1_genomic.fna/markers.fasta)
[2023-06-28 23:26:50,514] [INFO] Task started: Blastn
[2023-06-28 23:26:50,514] [INFO] Running command: blastn -query GCA_020717895.1_ASM2071789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c39c09-f77d-4876-890f-6d407202c903/dqc_reference/reference_markers_gtdb.fasta -out GCA_020717895.1_ASM2071789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:26:51,430] [INFO] Task succeeded: Blastn
[2023-06-28 23:26:51,435] [INFO] Selected 13 target genomes.
[2023-06-28 23:26:51,435] [INFO] Target genome list was writen to GCA_020717895.1_ASM2071789v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:26:51,439] [INFO] Task started: fastANI
[2023-06-28 23:26:51,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c50395d-6f50-4097-8089-6692a5595325/GCA_020717895.1_ASM2071789v1_genomic.fna.gz --refList GCA_020717895.1_ASM2071789v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020717895.1_ASM2071789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:26:59,896] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:59,908] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:26:59,909] [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_903875445.1	s__Desulforhopalus sp903875445	80.4845	661	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	99.93	99.88	0.93	0.87	5	-
GCA_018821785.1	s__Desulforhopalus sp018821785	80.3464	636	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391225.1	s__Desulforhopalus sp011391225	80.119	426	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961725.1	s__Desulforhopalus sp000961725	77.5617	319	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799365.1	s__Desulforhopalus sp001799365	77.3664	247	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000769715.1	s__Desulfoprunum sp000769715	76.7737	99	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.79	99.74	0.93	0.93	5	-
GCF_005116645.1	s__Desulforhopalus sp005116645	76.7189	164	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139415.1	s__Desulforhopalus sp013139415	76.0384	93	1553	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:26:59,911] [INFO] GTDB search result was written to GCA_020717895.1_ASM2071789v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:26:59,911] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:26:59,914] [INFO] DFAST_QC result json was written to GCA_020717895.1_ASM2071789v1_genomic.fna/dqc_result.json
[2023-06-28 23:26:59,914] [INFO] DFAST_QC completed!
[2023-06-28 23:26:59,914] [INFO] Total running time: 0h1m20s