[2023-06-19 08:42:04,240] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:42:04,243] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:42:04,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference
[2023-06-19 08:42:05,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:42:05,540] [INFO] Task started: Prodigal
[2023-06-19 08:42:05,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg65f4c47d-b196-47de-abbd-a35d6cde9a4d/GCA_013694935.1_ASM1369493v1_genomic.fna.gz | prodigal -d GCA_013694935.1_ASM1369493v1_genomic.fna/cds.fna -a GCA_013694935.1_ASM1369493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:42:18,577] [INFO] Task succeeded: Prodigal
[2023-06-19 08:42:18,577] [INFO] Task started: HMMsearch
[2023-06-19 08:42:18,577] [INFO] Running command: hmmsearch --tblout GCA_013694935.1_ASM1369493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference/reference_markers.hmm GCA_013694935.1_ASM1369493v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:42:18,888] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:42:18,889] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg65f4c47d-b196-47de-abbd-a35d6cde9a4d/GCA_013694935.1_ASM1369493v1_genomic.fna.gz]
[2023-06-19 08:42:18,937] [INFO] Query marker FASTA was written to GCA_013694935.1_ASM1369493v1_genomic.fna/markers.fasta
[2023-06-19 08:42:18,937] [INFO] Task started: Blastn
[2023-06-19 08:42:18,937] [INFO] Running command: blastn -query GCA_013694935.1_ASM1369493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference/reference_markers.fasta -out GCA_013694935.1_ASM1369493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:42:19,514] [INFO] Task succeeded: Blastn
[2023-06-19 08:42:19,521] [INFO] Selected 23 target genomes.
[2023-06-19 08:42:19,522] [INFO] Target genome list was writen to GCA_013694935.1_ASM1369493v1_genomic.fna/target_genomes.txt
[2023-06-19 08:42:19,529] [INFO] Task started: fastANI
[2023-06-19 08:42:19,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f4c47d-b196-47de-abbd-a35d6cde9a4d/GCA_013694935.1_ASM1369493v1_genomic.fna.gz --refList GCA_013694935.1_ASM1369493v1_genomic.fna/target_genomes.txt --output GCA_013694935.1_ASM1369493v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:42:39,270] [INFO] Task succeeded: fastANI
[2023-06-19 08:42:39,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:42:39,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:42:39,281] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:42:39,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:42:39,281] [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
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	76.2816	98	1380	95	below_threshold
Thermogemmatispora tikiterensis	strain=T81	GCA_003268475.1	1825093	1825093	type	True	76.1732	97	1380	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	75.9858	103	1380	95	below_threshold
Thermogemmatispora aurantia	strain=A1-2	GCA_008974285.1	2045279	2045279	type	True	75.9695	112	1380	95	below_threshold
Thermogemmatispora carboxidivorans	strain=PM5	GCA_000702505.1	1382306	1382306	type	True	75.7801	103	1380	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:42:39,287] [INFO] DFAST Taxonomy check result was written to GCA_013694935.1_ASM1369493v1_genomic.fna/tc_result.tsv
[2023-06-19 08:42:39,288] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:42:39,288] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:42:39,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference/checkm_data
[2023-06-19 08:42:39,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:42:39,353] [INFO] Task started: CheckM
[2023-06-19 08:42:39,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013694935.1_ASM1369493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013694935.1_ASM1369493v1_genomic.fna/checkm_input GCA_013694935.1_ASM1369493v1_genomic.fna/checkm_result
[2023-06-19 08:43:20,860] [INFO] Task succeeded: CheckM
[2023-06-19 08:43:20,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.99%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:43:20,893] [INFO] ===== Completeness check finished =====
[2023-06-19 08:43:20,893] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:43:20,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013694935.1_ASM1369493v1_genomic.fna/markers.fasta)
[2023-06-19 08:43:20,894] [INFO] Task started: Blastn
[2023-06-19 08:43:20,894] [INFO] Running command: blastn -query GCA_013694935.1_ASM1369493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266baa2a-fd40-4935-9fb8-50e1328db9f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_013694935.1_ASM1369493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:43:21,660] [INFO] Task succeeded: Blastn
[2023-06-19 08:43:21,666] [INFO] Selected 21 target genomes.
[2023-06-19 08:43:21,666] [INFO] Target genome list was writen to GCA_013694935.1_ASM1369493v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:43:21,700] [INFO] Task started: fastANI
[2023-06-19 08:43:21,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f4c47d-b196-47de-abbd-a35d6cde9a4d/GCA_013694935.1_ASM1369493v1_genomic.fna.gz --refList GCA_013694935.1_ASM1369493v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013694935.1_ASM1369493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:43:38,821] [INFO] Task succeeded: fastANI
[2023-06-19 08:43:38,836] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:43:38,837] [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_000178855.1	s__Ktedonobacter racemifer	77.2162	128	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587415.1	s__Ktedonobacter sp016587415	76.7713	131	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881495.1	s__UBA11361 sp005881495	76.7398	97	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810755.1	s__CADDYT01 sp902810755	76.5569	211	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695595.1	s__JACDAE01 sp013695595	76.5177	67	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__JACDAE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881995.1	s__CF-113 sp005881995	76.4727	84	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CF-113	95.0	97.86	97.86	0.74	0.74	2	-
GCF_016587375.1	s__Ktedonobacter sp016587375	76.3199	121	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812455.1	s__CADDZH01 sp902812455	76.3087	109	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDZH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	76.2038	88	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268475.1	s__Thermogemmatispora tikiterensis	76.1913	96	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	76.017	101	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974285.1	s__Thermogemmatispora aurantia	75.9704	112	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	99.32	99.32	0.97	0.97	2	-
GCF_001748285.1	s__Thermogemmatispora onikobensis	75.9155	108	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702505.1	s__Thermogemmatispora carboxidivorans	75.7801	103	1380	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:43:38,839] [INFO] GTDB search result was written to GCA_013694935.1_ASM1369493v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:43:38,840] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:43:38,846] [INFO] DFAST_QC result json was written to GCA_013694935.1_ASM1369493v1_genomic.fna/dqc_result.json
[2023-06-19 08:43:38,846] [INFO] DFAST_QC completed!
[2023-06-19 08:43:38,847] [INFO] Total running time: 0h1m35s