[2023-06-13 17:11:54,220] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:11:54,223] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:11:54,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference
[2023-06-13 17:11:55,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:11:55,616] [INFO] Task started: Prodigal
[2023-06-13 17:11:55,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg3593c1f7-6631-43bb-a019-775a12e5d8a1/GCA_022072455.1_ASM2207245v1_genomic.fna.gz | prodigal -d GCA_022072455.1_ASM2207245v1_genomic.fna/cds.fna -a GCA_022072455.1_ASM2207245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:15,144] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:15,144] [INFO] Task started: HMMsearch
[2023-06-13 17:12:15,144] [INFO] Running command: hmmsearch --tblout GCA_022072455.1_ASM2207245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference/reference_markers.hmm GCA_022072455.1_ASM2207245v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:15,445] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:15,447] [INFO] Found 6/6 markers.
[2023-06-13 17:12:15,512] [INFO] Query marker FASTA was written to GCA_022072455.1_ASM2207245v1_genomic.fna/markers.fasta
[2023-06-13 17:12:15,512] [INFO] Task started: Blastn
[2023-06-13 17:12:15,512] [INFO] Running command: blastn -query GCA_022072455.1_ASM2207245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference/reference_markers.fasta -out GCA_022072455.1_ASM2207245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:16,149] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:16,153] [INFO] Selected 24 target genomes.
[2023-06-13 17:12:16,153] [INFO] Target genome list was writen to GCA_022072455.1_ASM2207245v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:16,162] [INFO] Task started: fastANI
[2023-06-13 17:12:16,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg3593c1f7-6631-43bb-a019-775a12e5d8a1/GCA_022072455.1_ASM2207245v1_genomic.fna.gz --refList GCA_022072455.1_ASM2207245v1_genomic.fna/target_genomes.txt --output GCA_022072455.1_ASM2207245v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:34,228] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:34,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:34,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:34,231] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:34,231] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:12:34,232] [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
--------------------------------------------------------------------------------
[2023-06-13 17:12:34,234] [INFO] DFAST Taxonomy check result was written to GCA_022072455.1_ASM2207245v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:34,235] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:34,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:34,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference/checkm_data
[2023-06-13 17:12:34,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:34,289] [INFO] Task started: CheckM
[2023-06-13 17:12:34,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022072455.1_ASM2207245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022072455.1_ASM2207245v1_genomic.fna/checkm_input GCA_022072455.1_ASM2207245v1_genomic.fna/checkm_result
[2023-06-13 17:13:34,201] [INFO] Task succeeded: CheckM
[2023-06-13 17:13:34,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:13:34,227] [INFO] ===== Completeness check finished =====
[2023-06-13 17:13:34,227] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:13:34,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022072455.1_ASM2207245v1_genomic.fna/markers.fasta)
[2023-06-13 17:13:34,228] [INFO] Task started: Blastn
[2023-06-13 17:13:34,228] [INFO] Running command: blastn -query GCA_022072455.1_ASM2207245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg395c3463-67c7-4806-8491-ca40779a0538/dqc_reference/reference_markers_gtdb.fasta -out GCA_022072455.1_ASM2207245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:13:35,086] [INFO] Task succeeded: Blastn
[2023-06-13 17:13:35,091] [INFO] Selected 19 target genomes.
[2023-06-13 17:13:35,092] [INFO] Target genome list was writen to GCA_022072455.1_ASM2207245v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:13:35,109] [INFO] Task started: fastANI
[2023-06-13 17:13:35,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg3593c1f7-6631-43bb-a019-775a12e5d8a1/GCA_022072455.1_ASM2207245v1_genomic.fna.gz --refList GCA_022072455.1_ASM2207245v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022072455.1_ASM2207245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:46,606] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:46,619] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 17:13:46,619] [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_900299315.1	s__OMJI01 sp900299315	77.3083	188	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__OMJI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847335.1	s__CAINDI01 sp903847335	77.2349	145	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__CAINDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011374075.1	s__DRVI01 sp011374075	77.1804	172	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__DRVI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871575.1	s__CAIKAP01 sp016871575	76.9285	173	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__CAIKAP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825435.1	s__CAIKAP01 sp903825435	76.7181	159	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__CAIKAP01	95.0	99.89	99.81	0.94	0.94	3	-
GCA_003164675.1	s__Palsa-1439 sp003164675	76.6223	111	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__Palsa-1439	95.0	99.79	99.50	0.96	0.95	5	-
GCA_003152315.1	s__Palsa-1439 sp003152315	76.576	137	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__Palsa-1439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011373785.1	s__CAIKAP01 sp011373785	76.5431	110	1587	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Palsa-1439;f__Palsa-1439;g__CAIKAP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912445.1	s__DP16D-bin41 sp903912445	75.1991	59	1587	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__CAIQIC01;g__DP16D-bin41	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:46,621] [INFO] GTDB search result was written to GCA_022072455.1_ASM2207245v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:46,622] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:46,626] [INFO] DFAST_QC result json was written to GCA_022072455.1_ASM2207245v1_genomic.fna/dqc_result.json
[2023-06-13 17:13:46,627] [INFO] DFAST_QC completed!
[2023-06-13 17:13:46,627] [INFO] Total running time: 0h1m52s