[2023-06-18 23:17:45,065] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:17:45,072] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:17:45,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference
[2023-06-18 23:17:46,337] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:17:46,339] [INFO] Task started: Prodigal
[2023-06-18 23:17:46,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e7e72f1-5272-4c3d-a0bd-43aeaf0f17a3/GCA_013289945.1_ASM1328994v1_genomic.fna.gz | prodigal -d GCA_013289945.1_ASM1328994v1_genomic.fna/cds.fna -a GCA_013289945.1_ASM1328994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:17:52,260] [INFO] Task succeeded: Prodigal
[2023-06-18 23:17:52,261] [INFO] Task started: HMMsearch
[2023-06-18 23:17:52,261] [INFO] Running command: hmmsearch --tblout GCA_013289945.1_ASM1328994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference/reference_markers.hmm GCA_013289945.1_ASM1328994v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:17:52,492] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:17:52,493] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg7e7e72f1-5272-4c3d-a0bd-43aeaf0f17a3/GCA_013289945.1_ASM1328994v1_genomic.fna.gz]
[2023-06-18 23:17:52,522] [INFO] Query marker FASTA was written to GCA_013289945.1_ASM1328994v1_genomic.fna/markers.fasta
[2023-06-18 23:17:52,523] [INFO] Task started: Blastn
[2023-06-18 23:17:52,523] [INFO] Running command: blastn -query GCA_013289945.1_ASM1328994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference/reference_markers.fasta -out GCA_013289945.1_ASM1328994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:17:53,058] [INFO] Task succeeded: Blastn
[2023-06-18 23:17:53,068] [INFO] Selected 5 target genomes.
[2023-06-18 23:17:53,068] [INFO] Target genome list was writen to GCA_013289945.1_ASM1328994v1_genomic.fna/target_genomes.txt
[2023-06-18 23:17:53,070] [INFO] Task started: fastANI
[2023-06-18 23:17:53,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e7e72f1-5272-4c3d-a0bd-43aeaf0f17a3/GCA_013289945.1_ASM1328994v1_genomic.fna.gz --refList GCA_013289945.1_ASM1328994v1_genomic.fna/target_genomes.txt --output GCA_013289945.1_ASM1328994v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:17:55,412] [INFO] Task succeeded: fastANI
[2023-06-18 23:17:55,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:17:55,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:17:55,415] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:17:55,415] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 23:17:55,415] [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
--------------------------------------------------------------------------------
[2023-06-18 23:17:55,417] [INFO] DFAST Taxonomy check result was written to GCA_013289945.1_ASM1328994v1_genomic.fna/tc_result.tsv
[2023-06-18 23:17:55,418] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:17:55,418] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:17:55,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference/checkm_data
[2023-06-18 23:17:55,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:17:55,454] [INFO] Task started: CheckM
[2023-06-18 23:17:55,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013289945.1_ASM1328994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013289945.1_ASM1328994v1_genomic.fna/checkm_input GCA_013289945.1_ASM1328994v1_genomic.fna/checkm_result
[2023-06-18 23:18:19,088] [INFO] Task succeeded: CheckM
[2023-06-18 23:18:19,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:18:19,112] [INFO] ===== Completeness check finished =====
[2023-06-18 23:18:19,113] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:18:19,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013289945.1_ASM1328994v1_genomic.fna/markers.fasta)
[2023-06-18 23:18:19,114] [INFO] Task started: Blastn
[2023-06-18 23:18:19,114] [INFO] Running command: blastn -query GCA_013289945.1_ASM1328994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a8386b7-4136-4fcb-9a78-c64db6372d15/dqc_reference/reference_markers_gtdb.fasta -out GCA_013289945.1_ASM1328994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:19,707] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:19,711] [INFO] Selected 5 target genomes.
[2023-06-18 23:18:19,712] [INFO] Target genome list was writen to GCA_013289945.1_ASM1328994v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:18:19,716] [INFO] Task started: fastANI
[2023-06-18 23:18:19,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e7e72f1-5272-4c3d-a0bd-43aeaf0f17a3/GCA_013289945.1_ASM1328994v1_genomic.fna.gz --refList GCA_013289945.1_ASM1328994v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013289945.1_ASM1328994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:18:22,852] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:22,858] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 23:18:22,858] [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_002479255.1	s__Binatus soli	77.2032	112	556	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015478645.1	s__JADMIL01 sp015478645	76.8489	101	556	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JADMIL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135135.1	s__Binatus sp003135135	76.848	128	556	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__Binatus	95.0	99.92	99.78	0.98	0.97	5	-
GCA_011334465.1	s__DTIX01 sp011334465	76.7742	98	556	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__DTIX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237115.1	s__JAFAHS01 sp019237115	76.4477	87	556	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__Binatales;f__Binataceae;g__JAFAHS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:18:22,860] [INFO] GTDB search result was written to GCA_013289945.1_ASM1328994v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:18:22,861] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:18:22,864] [INFO] DFAST_QC result json was written to GCA_013289945.1_ASM1328994v1_genomic.fna/dqc_result.json
[2023-06-18 23:18:22,865] [INFO] DFAST_QC completed!
[2023-06-18 23:18:22,865] [INFO] Total running time: 0h0m38s