[2023-06-27 01:00:52,406] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:00:52,411] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:00:52,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference
[2023-06-27 01:00:54,922] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:00:54,923] [INFO] Task started: Prodigal
[2023-06-27 01:00:54,924] [INFO] Running command: gunzip -c /var/lib/cwl/stg060904ed-f6e6-405a-ab06-17258e72258c/GCA_026786155.1_ASM2678615v1_genomic.fna.gz | prodigal -d GCA_026786155.1_ASM2678615v1_genomic.fna/cds.fna -a GCA_026786155.1_ASM2678615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:01:01,659] [INFO] Task succeeded: Prodigal
[2023-06-27 01:01:01,659] [INFO] Task started: HMMsearch
[2023-06-27 01:01:01,660] [INFO] Running command: hmmsearch --tblout GCA_026786155.1_ASM2678615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference/reference_markers.hmm GCA_026786155.1_ASM2678615v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:01:01,906] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:01:01,908] [INFO] Found 6/6 markers.
[2023-06-27 01:01:01,999] [INFO] Query marker FASTA was written to GCA_026786155.1_ASM2678615v1_genomic.fna/markers.fasta
[2023-06-27 01:01:01,999] [INFO] Task started: Blastn
[2023-06-27 01:01:01,999] [INFO] Running command: blastn -query GCA_026786155.1_ASM2678615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference/reference_markers.fasta -out GCA_026786155.1_ASM2678615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:01:02,795] [INFO] Task succeeded: Blastn
[2023-06-27 01:01:02,799] [INFO] Selected 23 target genomes.
[2023-06-27 01:01:02,799] [INFO] Target genome list was writen to GCA_026786155.1_ASM2678615v1_genomic.fna/target_genomes.txt
[2023-06-27 01:01:02,807] [INFO] Task started: fastANI
[2023-06-27 01:01:02,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg060904ed-f6e6-405a-ab06-17258e72258c/GCA_026786155.1_ASM2678615v1_genomic.fna.gz --refList GCA_026786155.1_ASM2678615v1_genomic.fna/target_genomes.txt --output GCA_026786155.1_ASM2678615v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:01:17,251] [INFO] Task succeeded: fastANI
[2023-06-27 01:01:17,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:01:17,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:01:17,254] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:01:17,254] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 01:01:17,255] [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 01:01:17,257] [INFO] DFAST Taxonomy check result was written to GCA_026786155.1_ASM2678615v1_genomic.fna/tc_result.tsv
[2023-06-27 01:01:17,258] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:01:17,258] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:01:17,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference/checkm_data
[2023-06-27 01:01:17,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:01:17,298] [INFO] Task started: CheckM
[2023-06-27 01:01:17,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026786155.1_ASM2678615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026786155.1_ASM2678615v1_genomic.fna/checkm_input GCA_026786155.1_ASM2678615v1_genomic.fna/checkm_result
[2023-06-27 01:01:44,049] [INFO] Task succeeded: CheckM
[2023-06-27 01:01:44,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:01:44,074] [INFO] ===== Completeness check finished =====
[2023-06-27 01:01:44,075] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:01:44,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026786155.1_ASM2678615v1_genomic.fna/markers.fasta)
[2023-06-27 01:01:44,076] [INFO] Task started: Blastn
[2023-06-27 01:01:44,076] [INFO] Running command: blastn -query GCA_026786155.1_ASM2678615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68a77c25-f425-4389-a28e-5b2514255d3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_026786155.1_ASM2678615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:01:44,814] [INFO] Task succeeded: Blastn
[2023-06-27 01:01:44,818] [INFO] Selected 12 target genomes.
[2023-06-27 01:01:44,818] [INFO] Target genome list was writen to GCA_026786155.1_ASM2678615v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:01:44,855] [INFO] Task started: fastANI
[2023-06-27 01:01:44,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg060904ed-f6e6-405a-ab06-17258e72258c/GCA_026786155.1_ASM2678615v1_genomic.fna.gz --refList GCA_026786155.1_ASM2678615v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026786155.1_ASM2678615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:01:53,128] [INFO] Task succeeded: fastANI
[2023-06-27 01:01:53,137] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:01:53,137] [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_902805935.1	s__GCA-002050365 sp902805935	80.3336	478	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050365.1	s__GCA-002050365 sp002050365	79.3177	450	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	99.98	99.98	0.96	0.96	2	-
GCA_002050355.1	s__GCA-002050365 sp002050355	78.3287	315	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050455.1	s__GCA-002050365 sp002050455	78.2828	301	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	99.57	99.57	0.85	0.85	2	-
GCA_005790265.1	s__SXVE01 sp005790265	78.1598	306	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__SXVE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696385.1	s__GCA-002050365 sp013696385	78.0165	213	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018269075.1	s__JAFDVJ01 sp018269075	76.0092	161	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JAFDVJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715115.1	s__JAFDVJ01 sp016715115	75.5993	80	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JAFDVJ01	95.0	98.64	98.61	0.89	0.88	3	-
GCA_014379075.1	s__OLB17 sp014379075	75.5334	61	862	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 01:01:53,216] [INFO] GTDB search result was written to GCA_026786155.1_ASM2678615v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:01:53,235] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:01:53,239] [INFO] DFAST_QC result json was written to GCA_026786155.1_ASM2678615v1_genomic.fna/dqc_result.json
[2023-06-27 01:01:53,239] [INFO] DFAST_QC completed!
[2023-06-27 01:01:53,239] [INFO] Total running time: 0h1m1s