[2023-06-28 16:23:01,024] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:23:01,027] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:23:01,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference
[2023-06-28 16:23:02,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:23:02,230] [INFO] Task started: Prodigal
[2023-06-28 16:23:02,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg74e9b2a1-020e-4381-9700-e6835ba9fe91/GCA_017387945.1_ASM1738794v1_genomic.fna.gz | prodigal -d GCA_017387945.1_ASM1738794v1_genomic.fna/cds.fna -a GCA_017387945.1_ASM1738794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:23:06,825] [INFO] Task succeeded: Prodigal
[2023-06-28 16:23:06,825] [INFO] Task started: HMMsearch
[2023-06-28 16:23:06,825] [INFO] Running command: hmmsearch --tblout GCA_017387945.1_ASM1738794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference/reference_markers.hmm GCA_017387945.1_ASM1738794v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:23:06,960] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:23:06,961] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg74e9b2a1-020e-4381-9700-e6835ba9fe91/GCA_017387945.1_ASM1738794v1_genomic.fna.gz]
[2023-06-28 16:23:06,983] [INFO] Query marker FASTA was written to GCA_017387945.1_ASM1738794v1_genomic.fna/markers.fasta
[2023-06-28 16:23:06,983] [INFO] Task started: Blastn
[2023-06-28 16:23:06,983] [INFO] Running command: blastn -query GCA_017387945.1_ASM1738794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference/reference_markers.fasta -out GCA_017387945.1_ASM1738794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:23:07,487] [INFO] Task succeeded: Blastn
[2023-06-28 16:23:07,491] [INFO] Selected 6 target genomes.
[2023-06-28 16:23:07,491] [INFO] Target genome list was writen to GCA_017387945.1_ASM1738794v1_genomic.fna/target_genomes.txt
[2023-06-28 16:23:07,492] [INFO] Task started: fastANI
[2023-06-28 16:23:07,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e9b2a1-020e-4381-9700-e6835ba9fe91/GCA_017387945.1_ASM1738794v1_genomic.fna.gz --refList GCA_017387945.1_ASM1738794v1_genomic.fna/target_genomes.txt --output GCA_017387945.1_ASM1738794v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:23:10,764] [INFO] Task succeeded: fastANI
[2023-06-28 16:23:10,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:23:10,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:23:10,768] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:23:10,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:23:10,769] [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
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	78.4563	81	267	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:23:10,770] [INFO] DFAST Taxonomy check result was written to GCA_017387945.1_ASM1738794v1_genomic.fna/tc_result.tsv
[2023-06-28 16:23:10,771] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:23:10,771] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:23:10,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference/checkm_data
[2023-06-28 16:23:10,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:23:10,794] [INFO] Task started: CheckM
[2023-06-28 16:23:10,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017387945.1_ASM1738794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017387945.1_ASM1738794v1_genomic.fna/checkm_input GCA_017387945.1_ASM1738794v1_genomic.fna/checkm_result
[2023-06-28 16:23:29,742] [INFO] Task succeeded: CheckM
[2023-06-28 16:23:29,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:23:29,766] [INFO] ===== Completeness check finished =====
[2023-06-28 16:23:29,766] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:23:29,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017387945.1_ASM1738794v1_genomic.fna/markers.fasta)
[2023-06-28 16:23:29,767] [INFO] Task started: Blastn
[2023-06-28 16:23:29,767] [INFO] Running command: blastn -query GCA_017387945.1_ASM1738794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e55ae80-d90f-4b74-8907-380cb048a3bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_017387945.1_ASM1738794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:23:30,332] [INFO] Task succeeded: Blastn
[2023-06-28 16:23:30,336] [INFO] Selected 7 target genomes.
[2023-06-28 16:23:30,336] [INFO] Target genome list was writen to GCA_017387945.1_ASM1738794v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:23:30,338] [INFO] Task started: fastANI
[2023-06-28 16:23:30,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e9b2a1-020e-4381-9700-e6835ba9fe91/GCA_017387945.1_ASM1738794v1_genomic.fna.gz --refList GCA_017387945.1_ASM1738794v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017387945.1_ASM1738794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:23:33,349] [INFO] Task succeeded: fastANI
[2023-06-28 16:23:33,357] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:23:33,357] [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_016284885.1	s__Desulfovibrio sp016284885	98.2436	250	267	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.92	95.09	0.88	0.83	3	conclusive
GCA_002369295.1	s__Desulfovibrio sp002369295	90.3663	223	267	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.45	99.45	0.84	0.84	2	-
GCF_900116045.1	s__Desulfovibrio piger_A	78.5866	86	267	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCF_000156375.1	s__Desulfovibrio piger	78.5042	80	267	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCA_019113165.1	s__Desulfovibrio intestinipullorum	77.97	87	267	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:23:33,359] [INFO] GTDB search result was written to GCA_017387945.1_ASM1738794v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:23:33,360] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:23:33,362] [INFO] DFAST_QC result json was written to GCA_017387945.1_ASM1738794v1_genomic.fna/dqc_result.json
[2023-06-28 16:23:33,363] [INFO] DFAST_QC completed!
[2023-06-28 16:23:33,363] [INFO] Total running time: 0h0m32s