[2023-06-19 14:15:40,033] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:15:40,036] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:15:40,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference
[2023-06-19 14:15:41,257] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:15:41,258] [INFO] Task started: Prodigal
[2023-06-19 14:15:41,258] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4a465b6-c358-42ae-8b1c-497f4e374322/GCA_018058545.1_ASM1805854v1_genomic.fna.gz | prodigal -d GCA_018058545.1_ASM1805854v1_genomic.fna/cds.fna -a GCA_018058545.1_ASM1805854v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:15:51,090] [INFO] Task succeeded: Prodigal
[2023-06-19 14:15:51,091] [INFO] Task started: HMMsearch
[2023-06-19 14:15:51,091] [INFO] Running command: hmmsearch --tblout GCA_018058545.1_ASM1805854v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference/reference_markers.hmm GCA_018058545.1_ASM1805854v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:15:51,377] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:15:51,385] [INFO] Found 6/6 markers.
[2023-06-19 14:15:51,421] [INFO] Query marker FASTA was written to GCA_018058545.1_ASM1805854v1_genomic.fna/markers.fasta
[2023-06-19 14:15:51,421] [INFO] Task started: Blastn
[2023-06-19 14:15:51,421] [INFO] Running command: blastn -query GCA_018058545.1_ASM1805854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference/reference_markers.fasta -out GCA_018058545.1_ASM1805854v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:15:52,144] [INFO] Task succeeded: Blastn
[2023-06-19 14:15:52,149] [INFO] Selected 35 target genomes.
[2023-06-19 14:15:52,150] [INFO] Target genome list was writen to GCA_018058545.1_ASM1805854v1_genomic.fna/target_genomes.txt
[2023-06-19 14:15:52,229] [INFO] Task started: fastANI
[2023-06-19 14:15:52,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a465b6-c358-42ae-8b1c-497f4e374322/GCA_018058545.1_ASM1805854v1_genomic.fna.gz --refList GCA_018058545.1_ASM1805854v1_genomic.fna/target_genomes.txt --output GCA_018058545.1_ASM1805854v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:16:21,928] [INFO] Task succeeded: fastANI
[2023-06-19 14:16:21,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:16:21,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:16:21,940] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:16:21,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:16:21,940] [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
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.9046	78	1113	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	74.8278	56	1113	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.7933	62	1113	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	74.7682	53	1113	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	74.7476	75	1113	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.668	69	1113	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:16:21,942] [INFO] DFAST Taxonomy check result was written to GCA_018058545.1_ASM1805854v1_genomic.fna/tc_result.tsv
[2023-06-19 14:16:21,943] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:16:21,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:16:21,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference/checkm_data
[2023-06-19 14:16:21,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:16:21,986] [INFO] Task started: CheckM
[2023-06-19 14:16:21,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018058545.1_ASM1805854v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018058545.1_ASM1805854v1_genomic.fna/checkm_input GCA_018058545.1_ASM1805854v1_genomic.fna/checkm_result
[2023-06-19 14:16:54,435] [INFO] Task succeeded: CheckM
[2023-06-19 14:16:54,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:16:54,461] [INFO] ===== Completeness check finished =====
[2023-06-19 14:16:54,462] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:16:54,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018058545.1_ASM1805854v1_genomic.fna/markers.fasta)
[2023-06-19 14:16:54,462] [INFO] Task started: Blastn
[2023-06-19 14:16:54,463] [INFO] Running command: blastn -query GCA_018058545.1_ASM1805854v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc65e6a1b-23a4-4002-9803-23ff097ea7ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_018058545.1_ASM1805854v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:16:55,485] [INFO] Task succeeded: Blastn
[2023-06-19 14:16:55,491] [INFO] Selected 14 target genomes.
[2023-06-19 14:16:55,492] [INFO] Target genome list was writen to GCA_018058545.1_ASM1805854v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:16:55,503] [INFO] Task started: fastANI
[2023-06-19 14:16:55,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a465b6-c358-42ae-8b1c-497f4e374322/GCA_018058545.1_ASM1805854v1_genomic.fna.gz --refList GCA_018058545.1_ASM1805854v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018058545.1_ASM1805854v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:17:06,282] [INFO] Task succeeded: fastANI
[2023-06-19 14:17:06,298] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:17:06,299] [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_018058545.1	s__Promineofilum sp018058545	100.0	1103	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	99.89	99.89	0.93	0.93	2	conclusive
GCF_900066015.1	s__Promineofilum breve	79.49	639	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707605.1	s__Promineofilum sp016707605	79.3427	555	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983515.1	s__Promineofilum sp017983515	79.0009	375	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237545.1	s__Promineofilum sp014237545	79.0002	462	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123775.1	s__SLGK01 sp007123775	76.0058	81	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__SLGK01	95.0	99.66	99.66	0.91	0.91	2	-
GCA_012515125.1	s__JAAYYY01 sp012515125	75.9505	96	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__JAAYYY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705235.1	s__JADJXA01 sp016705235	75.8995	85	1113	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__JADJXA01	95.0	99.13	98.95	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2023-06-19 14:17:06,301] [INFO] GTDB search result was written to GCA_018058545.1_ASM1805854v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:17:06,302] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:17:06,309] [INFO] DFAST_QC result json was written to GCA_018058545.1_ASM1805854v1_genomic.fna/dqc_result.json
[2023-06-19 14:17:06,309] [INFO] DFAST_QC completed!
[2023-06-19 14:17:06,309] [INFO] Total running time: 0h1m26s