[2024-01-24 12:06:33,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,512] [INFO] DQC Reference Directory: /var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference
[2024-01-24 12:06:34,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,820] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f3f694d-5659-42c8-9676-69a8be32bc6e/GCF_001613545.1_ASM161354v1_genomic.fna.gz | prodigal -d GCF_001613545.1_ASM161354v1_genomic.fna/cds.fna -a GCF_001613545.1_ASM161354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:04,110] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:04,111] [INFO] Task started: HMMsearch
[2024-01-24 12:07:04,111] [INFO] Running command: hmmsearch --tblout GCF_001613545.1_ASM161354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference/reference_markers.hmm GCF_001613545.1_ASM161354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:04,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:04,385] [INFO] Found 6/6 markers.
[2024-01-24 12:07:04,427] [INFO] Query marker FASTA was written to GCF_001613545.1_ASM161354v1_genomic.fna/markers.fasta
[2024-01-24 12:07:04,427] [INFO] Task started: Blastn
[2024-01-24 12:07:04,427] [INFO] Running command: blastn -query GCF_001613545.1_ASM161354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference/reference_markers.fasta -out GCF_001613545.1_ASM161354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:05,062] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:05,066] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:05,067] [INFO] Target genome list was writen to GCF_001613545.1_ASM161354v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:05,075] [INFO] Task started: fastANI
[2024-01-24 12:07:05,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3f694d-5659-42c8-9676-69a8be32bc6e/GCF_001613545.1_ASM161354v1_genomic.fna.gz --refList GCF_001613545.1_ASM161354v1_genomic.fna/target_genomes.txt --output GCF_001613545.1_ASM161354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:17,242] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:17,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:17,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:17,253] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:17,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:17,254] [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
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	100.0	1582	1583	95	conclusive
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.9191	96	1583	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.8757	96	1583	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.7229	68	1583	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	76.373	53	1583	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.0866	68	1583	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.1231	60	1583	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	74.7616	63	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:17,255] [INFO] DFAST Taxonomy check result was written to GCF_001613545.1_ASM161354v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:17,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:17,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:17,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference/checkm_data
[2024-01-24 12:07:17,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:17,304] [INFO] Task started: CheckM
[2024-01-24 12:07:17,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613545.1_ASM161354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613545.1_ASM161354v1_genomic.fna/checkm_input GCF_001613545.1_ASM161354v1_genomic.fna/checkm_result
[2024-01-24 12:08:34,053] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:34,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:34,074] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:34,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:34,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613545.1_ASM161354v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:34,075] [INFO] Task started: Blastn
[2024-01-24 12:08:34,076] [INFO] Running command: blastn -query GCF_001613545.1_ASM161354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee953ac0-756b-4836-bc26-3b2bc8fd6066/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613545.1_ASM161354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:34,995] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:34,999] [INFO] Selected 12 target genomes.
[2024-01-24 12:08:34,999] [INFO] Target genome list was writen to GCF_001613545.1_ASM161354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:35,031] [INFO] Task started: fastANI
[2024-01-24 12:08:35,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3f694d-5659-42c8-9676-69a8be32bc6e/GCF_001613545.1_ASM161354v1_genomic.fna.gz --refList GCF_001613545.1_ASM161354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613545.1_ASM161354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:44,035] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:44,045] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:44,046] [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
GCF_001613545.1	s__Terrimicrobium sacchariphilum	100.0	1582	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003054655.1	s__Terrimicrobium sp003054655	88.2843	1120	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305195.1	s__Terrimicrobium sp001897195	86.8292	1106	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	99.90	99.90	0.94	0.94	2	-
GCA_018402345.1	s__UBA967 sp018402345	77.2939	101	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970255.1	s__UBA967 sp018970255	77.1915	123	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655545.1	s__JAATET01 sp015655545	76.7785	134	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JAATET01;g__JAATET01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280915.1	s__QYQL01 sp007280915	76.5908	104	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240025.1	s__SZAS-18 sp018240025	76.3176	85	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__SZAS-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903874975.1	s__Chthoniobacter sp903874975	76.2767	83	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	97.99	97.82	0.84	0.83	3	-
GCA_009885995.1	s__VFJQ01 sp009885995	76.0853	106	1583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__VFJQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:44,047] [INFO] GTDB search result was written to GCF_001613545.1_ASM161354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:44,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:44,050] [INFO] DFAST_QC result json was written to GCF_001613545.1_ASM161354v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:44,051] [INFO] DFAST_QC completed!
[2024-01-24 12:08:44,051] [INFO] Total running time: 0h2m11s