[2023-06-29 00:23:08,745] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:23:08,750] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:23:08,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference
[2023-06-29 00:23:10,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:23:10,539] [INFO] Task started: Prodigal
[2023-06-29 00:23:10,539] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9249e13-466a-4326-ae34-2bc31e6c7b85/GCA_020072925.1_ASM2007292v1_genomic.fna.gz | prodigal -d GCA_020072925.1_ASM2007292v1_genomic.fna/cds.fna -a GCA_020072925.1_ASM2007292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:23:27,617] [INFO] Task succeeded: Prodigal
[2023-06-29 00:23:27,617] [INFO] Task started: HMMsearch
[2023-06-29 00:23:27,617] [INFO] Running command: hmmsearch --tblout GCA_020072925.1_ASM2007292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference/reference_markers.hmm GCA_020072925.1_ASM2007292v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:23:27,958] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:23:27,960] [INFO] Found 6/6 markers.
[2023-06-29 00:23:28,038] [INFO] Query marker FASTA was written to GCA_020072925.1_ASM2007292v1_genomic.fna/markers.fasta
[2023-06-29 00:23:28,038] [INFO] Task started: Blastn
[2023-06-29 00:23:28,038] [INFO] Running command: blastn -query GCA_020072925.1_ASM2007292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference/reference_markers.fasta -out GCA_020072925.1_ASM2007292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:23:28,688] [INFO] Task succeeded: Blastn
[2023-06-29 00:23:28,700] [INFO] Selected 25 target genomes.
[2023-06-29 00:23:28,701] [INFO] Target genome list was writen to GCA_020072925.1_ASM2007292v1_genomic.fna/target_genomes.txt
[2023-06-29 00:23:28,709] [INFO] Task started: fastANI
[2023-06-29 00:23:28,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9249e13-466a-4326-ae34-2bc31e6c7b85/GCA_020072925.1_ASM2007292v1_genomic.fna.gz --refList GCA_020072925.1_ASM2007292v1_genomic.fna/target_genomes.txt --output GCA_020072925.1_ASM2007292v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:23:48,566] [INFO] Task succeeded: fastANI
[2023-06-29 00:23:48,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:23:48,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:23:48,579] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:23:48,579] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:23:48,580] [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
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	74.925	55	1943	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	74.9153	56	1943	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	74.9146	56	1943	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=ATCC 10970	GCA_000331185.2	132474	1927	type	True	74.8104	51	1943	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=NRRL ISP-5260	GCA_000717285.1	132474	1927	type	True	74.7018	50	1943	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.6491	57	1943	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:23:48,583] [INFO] DFAST Taxonomy check result was written to GCA_020072925.1_ASM2007292v1_genomic.fna/tc_result.tsv
[2023-06-29 00:23:48,584] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:23:48,584] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:23:48,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference/checkm_data
[2023-06-29 00:23:48,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:23:48,649] [INFO] Task started: CheckM
[2023-06-29 00:23:48,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020072925.1_ASM2007292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020072925.1_ASM2007292v1_genomic.fna/checkm_input GCA_020072925.1_ASM2007292v1_genomic.fna/checkm_result
[2023-06-29 00:24:38,446] [INFO] Task succeeded: CheckM
[2023-06-29 00:24:38,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:24:38,479] [INFO] ===== Completeness check finished =====
[2023-06-29 00:24:38,479] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:24:38,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020072925.1_ASM2007292v1_genomic.fna/markers.fasta)
[2023-06-29 00:24:38,480] [INFO] Task started: Blastn
[2023-06-29 00:24:38,480] [INFO] Running command: blastn -query GCA_020072925.1_ASM2007292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59849c6f-93ea-4f7d-8812-c46908f5e3cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_020072925.1_ASM2007292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:24:39,309] [INFO] Task succeeded: Blastn
[2023-06-29 00:24:39,314] [INFO] Selected 25 target genomes.
[2023-06-29 00:24:39,314] [INFO] Target genome list was writen to GCA_020072925.1_ASM2007292v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:24:39,319] [INFO] Task started: fastANI
[2023-06-29 00:24:39,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9249e13-466a-4326-ae34-2bc31e6c7b85/GCA_020072925.1_ASM2007292v1_genomic.fna.gz --refList GCA_020072925.1_ASM2007292v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020072925.1_ASM2007292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:24:56,865] [INFO] Task succeeded: fastANI
[2023-06-29 00:24:56,882] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:24:56,883] [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_002478145.1	s__UBA7540 sp002478145	76.6612	210	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__UBA7540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812365.1	s__CADDZC01 sp902812365	76.6403	87	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__CADDZC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003225365.1	s__Gp13-AA74 sp003225365	76.4788	159	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Gp13-AA74	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003224665.1	s__QHZM01 sp003224665	76.4548	98	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__QHZM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202975.1	s__JACQNR01 sp016202975	76.413	118	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__JACQNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003224635.1	s__Gp13-AA77 sp003224635	76.3853	149	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Gp13-AA77	95.0	98.46	98.46	0.78	0.78	2	-
GCA_003224695.1	s__Gp13-AA74 sp003224695	76.1336	158	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Gp13-AA74	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165615.1	s__Bog-366 sp003165615	76.0544	146	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Bog-366	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812465.1	s__CADDZE01 sp902812465	76.0526	103	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__CADDZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812415.1	s__RH2-MAG17b sp902812415	76.0366	97	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__RH2-MAG17b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165315.1	s__Bog-366 sp003165315	75.8297	114	1943	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__UBA7540;f__UBA7540;g__Bog-366	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:24:56,886] [INFO] GTDB search result was written to GCA_020072925.1_ASM2007292v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:24:56,887] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:24:56,890] [INFO] DFAST_QC result json was written to GCA_020072925.1_ASM2007292v1_genomic.fna/dqc_result.json
[2023-06-29 00:24:56,890] [INFO] DFAST_QC completed!
[2023-06-29 00:24:56,891] [INFO] Total running time: 0h1m48s