[2024-01-25 19:39:05,710] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:05,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:05,712] [INFO] DQC Reference Directory: /var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference
[2024-01-25 19:39:06,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:06,936] [INFO] Task started: Prodigal
[2024-01-25 19:39:06,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg0be2492b-3d12-45a6-8ded-a0c19562f75d/GCF_003385075.1_ASM338507v1_genomic.fna.gz | prodigal -d GCF_003385075.1_ASM338507v1_genomic.fna/cds.fna -a GCF_003385075.1_ASM338507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:20,015] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:20,016] [INFO] Task started: HMMsearch
[2024-01-25 19:39:20,016] [INFO] Running command: hmmsearch --tblout GCF_003385075.1_ASM338507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference/reference_markers.hmm GCF_003385075.1_ASM338507v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:20,331] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:20,332] [INFO] Found 6/6 markers.
[2024-01-25 19:39:20,359] [INFO] Query marker FASTA was written to GCF_003385075.1_ASM338507v1_genomic.fna/markers.fasta
[2024-01-25 19:39:20,359] [INFO] Task started: Blastn
[2024-01-25 19:39:20,360] [INFO] Running command: blastn -query GCF_003385075.1_ASM338507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference/reference_markers.fasta -out GCF_003385075.1_ASM338507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:20,921] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:20,923] [INFO] Selected 16 target genomes.
[2024-01-25 19:39:20,924] [INFO] Target genome list was writen to GCF_003385075.1_ASM338507v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:20,954] [INFO] Task started: fastANI
[2024-01-25 19:39:20,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg0be2492b-3d12-45a6-8ded-a0c19562f75d/GCF_003385075.1_ASM338507v1_genomic.fna.gz --refList GCF_003385075.1_ASM338507v1_genomic.fna/target_genomes.txt --output GCF_003385075.1_ASM338507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:31,180] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:31,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:31,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:31,186] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:39:31,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:31,186] [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
Pelolinea submarina	strain=DSM 23923	GCA_003385075.1	913107	913107	type	True	100.0	1167	1169	95	conclusive
Pelolinea submarina	strain=MO-CFX1	GCA_003966975.1	913107	913107	type	True	99.996	1169	1169	95	conclusive
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	77.0248	53	1169	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	76.848	61	1169	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	76.0536	56	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:31,188] [INFO] DFAST Taxonomy check result was written to GCF_003385075.1_ASM338507v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:31,188] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:31,188] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:31,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference/checkm_data
[2024-01-25 19:39:31,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:31,224] [INFO] Task started: CheckM
[2024-01-25 19:39:31,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385075.1_ASM338507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385075.1_ASM338507v1_genomic.fna/checkm_input GCF_003385075.1_ASM338507v1_genomic.fna/checkm_result
[2024-01-25 19:40:12,570] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:12,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:12,590] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:12,590] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:12,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385075.1_ASM338507v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:12,592] [INFO] Task started: Blastn
[2024-01-25 19:40:12,592] [INFO] Running command: blastn -query GCF_003385075.1_ASM338507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebbc483a-0a18-4c83-b7af-8960f2d9424a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385075.1_ASM338507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:13,418] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:13,422] [INFO] Selected 18 target genomes.
[2024-01-25 19:40:13,422] [INFO] Target genome list was writen to GCF_003385075.1_ASM338507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:13,455] [INFO] Task started: fastANI
[2024-01-25 19:40:13,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg0be2492b-3d12-45a6-8ded-a0c19562f75d/GCF_003385075.1_ASM338507v1_genomic.fna.gz --refList GCF_003385075.1_ASM338507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385075.1_ASM338507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:22,971] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:22,976] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:22,976] [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_003966975.1	s__Pelolinea submarina	99.996	1169	1169	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Pelolinea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002412595.1	s__Pelolinea sp002412595	81.5599	617	1169	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Pelolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178095.1	s__Pelolinea sp013178095	78.1703	352	1169	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Pelolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306035.1	s__Levilinea saccharolytica	77.0248	53	1169	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	-
GCF_001306115.1	s__Ornatilinea apprima	76.0536	56	1169	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Ornatilinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:22,977] [INFO] GTDB search result was written to GCF_003385075.1_ASM338507v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:22,978] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:22,984] [INFO] DFAST_QC result json was written to GCF_003385075.1_ASM338507v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:22,984] [INFO] DFAST_QC completed!
[2024-01-25 19:40:22,984] [INFO] Total running time: 0h1m17s