[2023-06-29 09:20:03,451] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:20:03,453] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:20:03,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference
[2023-06-29 09:20:04,917] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:20:04,919] [INFO] Task started: Prodigal
[2023-06-29 09:20:04,919] [INFO] Running command: gunzip -c /var/lib/cwl/stge98e089e-f48c-4226-8ade-c93bbd3efe41/GCA_027486095.1_ASM2748609v1_genomic.fna.gz | prodigal -d GCA_027486095.1_ASM2748609v1_genomic.fna/cds.fna -a GCA_027486095.1_ASM2748609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:20:15,164] [INFO] Task succeeded: Prodigal
[2023-06-29 09:20:15,165] [INFO] Task started: HMMsearch
[2023-06-29 09:20:15,165] [INFO] Running command: hmmsearch --tblout GCA_027486095.1_ASM2748609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference/reference_markers.hmm GCA_027486095.1_ASM2748609v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:20:15,415] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:20:15,416] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge98e089e-f48c-4226-8ade-c93bbd3efe41/GCA_027486095.1_ASM2748609v1_genomic.fna.gz]
[2023-06-29 09:20:15,452] [INFO] Query marker FASTA was written to GCA_027486095.1_ASM2748609v1_genomic.fna/markers.fasta
[2023-06-29 09:20:15,453] [INFO] Task started: Blastn
[2023-06-29 09:20:15,453] [INFO] Running command: blastn -query GCA_027486095.1_ASM2748609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference/reference_markers.fasta -out GCA_027486095.1_ASM2748609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:20:16,031] [INFO] Task succeeded: Blastn
[2023-06-29 09:20:16,035] [INFO] Selected 11 target genomes.
[2023-06-29 09:20:16,035] [INFO] Target genome list was writen to GCA_027486095.1_ASM2748609v1_genomic.fna/target_genomes.txt
[2023-06-29 09:20:16,049] [INFO] Task started: fastANI
[2023-06-29 09:20:16,050] [INFO] Running command: fastANI --query /var/lib/cwl/stge98e089e-f48c-4226-8ade-c93bbd3efe41/GCA_027486095.1_ASM2748609v1_genomic.fna.gz --refList GCA_027486095.1_ASM2748609v1_genomic.fna/target_genomes.txt --output GCA_027486095.1_ASM2748609v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:20:28,123] [INFO] Task succeeded: fastANI
[2023-06-29 09:20:28,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:20:28,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:20:28,132] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:20:28,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:20:28,133] [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
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.253	101	1032	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.0652	99	1032	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.9854	127	1032	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.7665	52	1032	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.7512	95	1032	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.6408	90	1032	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0227	125	1032	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	74.7885	66	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:20:28,135] [INFO] DFAST Taxonomy check result was written to GCA_027486095.1_ASM2748609v1_genomic.fna/tc_result.tsv
[2023-06-29 09:20:28,136] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:20:28,136] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:20:28,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference/checkm_data
[2023-06-29 09:20:28,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:20:28,181] [INFO] Task started: CheckM
[2023-06-29 09:20:28,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027486095.1_ASM2748609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027486095.1_ASM2748609v1_genomic.fna/checkm_input GCA_027486095.1_ASM2748609v1_genomic.fna/checkm_result
[2023-06-29 09:21:04,221] [INFO] Task succeeded: CheckM
[2023-06-29 09:21:04,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.14%
Contamintation: 8.80%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 09:21:04,250] [INFO] ===== Completeness check finished =====
[2023-06-29 09:21:04,250] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:21:04,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027486095.1_ASM2748609v1_genomic.fna/markers.fasta)
[2023-06-29 09:21:04,251] [INFO] Task started: Blastn
[2023-06-29 09:21:04,251] [INFO] Running command: blastn -query GCA_027486095.1_ASM2748609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35408d49-5707-4236-83b6-26507d6b8200/dqc_reference/reference_markers_gtdb.fasta -out GCA_027486095.1_ASM2748609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:21:05,025] [INFO] Task succeeded: Blastn
[2023-06-29 09:21:05,030] [INFO] Selected 10 target genomes.
[2023-06-29 09:21:05,030] [INFO] Target genome list was writen to GCA_027486095.1_ASM2748609v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:21:05,037] [INFO] Task started: fastANI
[2023-06-29 09:21:05,038] [INFO] Running command: fastANI --query /var/lib/cwl/stge98e089e-f48c-4226-8ade-c93bbd3efe41/GCA_027486095.1_ASM2748609v1_genomic.fna.gz --refList GCA_027486095.1_ASM2748609v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027486095.1_ASM2748609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:21:12,825] [INFO] Task succeeded: fastANI
[2023-06-29 09:21:12,835] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:21:12,835] [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_009926295.1	s__RGVT01 sp009926295	81.8651	530	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	81.8264	418	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	81.5193	382	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	79.5128	374	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	79.4	317	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	79.219	402	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	79.1124	368	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_903831155.1	s__QWPN01 sp903831155	79.0054	420	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885855.1	s__QWOP01 sp903885855	78.0196	343	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903949225.1	s__QWOP01 sp903949225	77.5472	260	1032	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:21:12,837] [INFO] GTDB search result was written to GCA_027486095.1_ASM2748609v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:21:12,838] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:21:12,842] [INFO] DFAST_QC result json was written to GCA_027486095.1_ASM2748609v1_genomic.fna/dqc_result.json
[2023-06-29 09:21:12,842] [INFO] DFAST_QC completed!
[2023-06-29 09:21:12,842] [INFO] Total running time: 0h1m9s