[2024-01-24 11:26:54,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference
[2024-01-24 11:26:58,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,222] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,222] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b2b634b-5123-4ca8-8934-1a19d5d24d83/GCF_001050235.1_ASM105023v2_genomic.fna.gz | prodigal -d GCF_001050235.1_ASM105023v2_genomic.fna/cds.fna -a GCF_001050235.1_ASM105023v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:11,538] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:11,539] [INFO] Task started: HMMsearch
[2024-01-24 11:27:11,539] [INFO] Running command: hmmsearch --tblout GCF_001050235.1_ASM105023v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference/reference_markers.hmm GCF_001050235.1_ASM105023v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:11,840] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:11,842] [INFO] Found 6/6 markers.
[2024-01-24 11:27:11,887] [INFO] Query marker FASTA was written to GCF_001050235.1_ASM105023v2_genomic.fna/markers.fasta
[2024-01-24 11:27:11,888] [INFO] Task started: Blastn
[2024-01-24 11:27:11,888] [INFO] Running command: blastn -query GCF_001050235.1_ASM105023v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference/reference_markers.fasta -out GCF_001050235.1_ASM105023v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:12,487] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:12,490] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:12,491] [INFO] Target genome list was writen to GCF_001050235.1_ASM105023v2_genomic.fna/target_genomes.txt
[2024-01-24 11:27:12,498] [INFO] Task started: fastANI
[2024-01-24 11:27:12,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b2b634b-5123-4ca8-8934-1a19d5d24d83/GCF_001050235.1_ASM105023v2_genomic.fna.gz --refList GCF_001050235.1_ASM105023v2_genomic.fna/target_genomes.txt --output GCF_001050235.1_ASM105023v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:26,387] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:26,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:26,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:26,397] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:26,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:26,398] [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
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	100.0	1476	1478	95	conclusive
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	77.1803	142	1478	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	76.9933	140	1478	95	below_threshold
Anaerolinea thermophila	strain=UNI-1	GCA_000199675.1	167964	167964	type	True	76.5042	64	1478	95	below_threshold
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	75.6657	54	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:26,399] [INFO] DFAST Taxonomy check result was written to GCF_001050235.1_ASM105023v2_genomic.fna/tc_result.tsv
[2024-01-24 11:27:26,400] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:26,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:26,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference/checkm_data
[2024-01-24 11:27:26,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:26,441] [INFO] Task started: CheckM
[2024-01-24 11:27:26,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050235.1_ASM105023v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050235.1_ASM105023v2_genomic.fna/checkm_input GCF_001050235.1_ASM105023v2_genomic.fna/checkm_result
[2024-01-24 11:28:07,832] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:07,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:07,854] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:07,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:07,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050235.1_ASM105023v2_genomic.fna/markers.fasta)
[2024-01-24 11:28:07,855] [INFO] Task started: Blastn
[2024-01-24 11:28:07,855] [INFO] Running command: blastn -query GCF_001050235.1_ASM105023v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e13aa13-1409-4640-b4f9-25017ced6571/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050235.1_ASM105023v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:08,753] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:08,757] [INFO] Selected 18 target genomes.
[2024-01-24 11:28:08,757] [INFO] Target genome list was writen to GCF_001050235.1_ASM105023v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:08,825] [INFO] Task started: fastANI
[2024-01-24 11:28:08,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b2b634b-5123-4ca8-8934-1a19d5d24d83/GCF_001050235.1_ASM105023v2_genomic.fna.gz --refList GCF_001050235.1_ASM105023v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001050235.1_ASM105023v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:20,911] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:20,925] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:20,925] [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_001050235.1	s__Longilinea arvoryzae	100.0	1477	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Longilinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004347695.1	s__Bellilinea sp004347695	77.3093	99	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Bellilinea	95.0	98.75	98.75	0.96	0.96	2	-
GCF_001306035.1	s__Levilinea saccharolytica	77.0098	139	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	-
GCA_009772985.1	s__UBA877 sp009772985	76.754	86	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385985.1	s__UBA3924 sp002385985	76.5647	112	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	-
GCF_000199675.1	s__Anaerolinea thermophila	76.5106	65	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798515.1	s__JAAZNB01 sp012798515	76.505	97	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__JAAZNB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298885.1	s__UBA700 sp002298885	76.4872	120	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA700	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012797695.1	s__UBA6107 sp012797695	76.4122	76	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA6107	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297445.1	s__SCUK01 sp004297445	76.1407	65	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__SCUK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428565.1	s__UBA6092 sp002428565	76.1248	113	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875215.1	s__UBA5195 sp903875215	75.9942	76	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.98	99.95	0.99	0.97	6	-
GCA_016927865.1	s__Anaerolinea sp016927865	75.9939	92	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516075.1	s__JAAYXE01 sp012516075	75.3727	74	1478	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__JAAYXE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:20,927] [INFO] GTDB search result was written to GCF_001050235.1_ASM105023v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:20,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:20,931] [INFO] DFAST_QC result json was written to GCF_001050235.1_ASM105023v2_genomic.fna/dqc_result.json
[2024-01-24 11:28:20,931] [INFO] DFAST_QC completed!
[2024-01-24 11:28:20,931] [INFO] Total running time: 0h1m27s