[2023-06-18 11:02:13,711] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:02:13,713] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:02:13,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference
[2023-06-18 11:02:14,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:02:14,950] [INFO] Task started: Prodigal
[2023-06-18 11:02:14,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg94954f8b-08f4-4eab-9b91-c65aa34d2e71/GCA_014379745.1_ASM1437974v1_genomic.fna.gz | prodigal -d GCA_014379745.1_ASM1437974v1_genomic.fna/cds.fna -a GCA_014379745.1_ASM1437974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:02:25,243] [INFO] Task succeeded: Prodigal
[2023-06-18 11:02:25,244] [INFO] Task started: HMMsearch
[2023-06-18 11:02:25,244] [INFO] Running command: hmmsearch --tblout GCA_014379745.1_ASM1437974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference/reference_markers.hmm GCA_014379745.1_ASM1437974v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:02:25,526] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:02:25,528] [INFO] Found 6/6 markers.
[2023-06-18 11:02:25,575] [INFO] Query marker FASTA was written to GCA_014379745.1_ASM1437974v1_genomic.fna/markers.fasta
[2023-06-18 11:02:25,576] [INFO] Task started: Blastn
[2023-06-18 11:02:25,576] [INFO] Running command: blastn -query GCA_014379745.1_ASM1437974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference/reference_markers.fasta -out GCA_014379745.1_ASM1437974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:02:26,175] [INFO] Task succeeded: Blastn
[2023-06-18 11:02:26,180] [INFO] Selected 30 target genomes.
[2023-06-18 11:02:26,180] [INFO] Target genome list was writen to GCA_014379745.1_ASM1437974v1_genomic.fna/target_genomes.txt
[2023-06-18 11:02:26,219] [INFO] Task started: fastANI
[2023-06-18 11:02:26,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg94954f8b-08f4-4eab-9b91-c65aa34d2e71/GCA_014379745.1_ASM1437974v1_genomic.fna.gz --refList GCA_014379745.1_ASM1437974v1_genomic.fna/target_genomes.txt --output GCA_014379745.1_ASM1437974v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:02:45,269] [INFO] Task succeeded: fastANI
[2023-06-18 11:02:45,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:02:45,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:02:45,279] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:02:45,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:02:45,279] [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
Pyrinomonas methylaliphatogenes	strain=type strain:K22	GCA_000820845.2	454194	454194	type	True	75.6708	91	1065	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	74.6209	50	1065	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	74.4921	55	1065	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:02:45,282] [INFO] DFAST Taxonomy check result was written to GCA_014379745.1_ASM1437974v1_genomic.fna/tc_result.tsv
[2023-06-18 11:02:45,282] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:02:45,283] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:02:45,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference/checkm_data
[2023-06-18 11:02:45,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:02:45,339] [INFO] Task started: CheckM
[2023-06-18 11:02:45,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014379745.1_ASM1437974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014379745.1_ASM1437974v1_genomic.fna/checkm_input GCA_014379745.1_ASM1437974v1_genomic.fna/checkm_result
[2023-06-18 11:03:19,744] [INFO] Task succeeded: CheckM
[2023-06-18 11:03:19,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.45%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 11:03:19,782] [INFO] ===== Completeness check finished =====
[2023-06-18 11:03:19,782] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:03:19,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014379745.1_ASM1437974v1_genomic.fna/markers.fasta)
[2023-06-18 11:03:19,783] [INFO] Task started: Blastn
[2023-06-18 11:03:19,783] [INFO] Running command: blastn -query GCA_014379745.1_ASM1437974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9df51ea7-f3a8-4610-a8bf-ab8b1377fb26/dqc_reference/reference_markers_gtdb.fasta -out GCA_014379745.1_ASM1437974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:20,596] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:20,601] [INFO] Selected 14 target genomes.
[2023-06-18 11:03:20,601] [INFO] Target genome list was writen to GCA_014379745.1_ASM1437974v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:03:20,611] [INFO] Task started: fastANI
[2023-06-18 11:03:20,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg94954f8b-08f4-4eab-9b91-c65aa34d2e71/GCA_014379745.1_ASM1437974v1_genomic.fna.gz --refList GCA_014379745.1_ASM1437974v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014379745.1_ASM1437974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:03:31,064] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:31,080] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 11:03:31,081] [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_003222975.1	s__QHXN01 sp003222975	81.5527	622	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242475.1	s__QHXN01 sp019242475	79.9729	558	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239425.1	s__QHXN01 sp019239425	79.7903	606	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223935.1	s__QHXQ01 sp003223935	77.151	254	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247865.1	s__JACMLC01 sp019247865	76.8495	174	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACMLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816505.1	s__JACDEG01 sp013816505	76.7309	235	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACDEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813825.1	s__JACCRA01 sp013813825	76.5829	165	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACCRA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698055.1	s__QHXM01 sp013698055	76.5406	96	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696465.1	s__JACCYN01 sp013696465	76.2598	118	1065	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACCYN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:03:31,090] [INFO] GTDB search result was written to GCA_014379745.1_ASM1437974v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:03:31,091] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:03:31,095] [INFO] DFAST_QC result json was written to GCA_014379745.1_ASM1437974v1_genomic.fna/dqc_result.json
[2023-06-18 11:03:31,095] [INFO] DFAST_QC completed!
[2023-06-18 11:03:31,095] [INFO] Total running time: 0h1m17s