[2024-01-24 12:44:43,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,423] [INFO] DQC Reference Directory: /var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference
[2024-01-24 12:44:44,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,923] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,923] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4ad21a2-1aef-4862-83bd-92ccd23a6e1a/GCF_016907925.1_ASM1690792v1_genomic.fna.gz | prodigal -d GCF_016907925.1_ASM1690792v1_genomic.fna/cds.fna -a GCF_016907925.1_ASM1690792v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:07,949] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:07,949] [INFO] Task started: HMMsearch
[2024-01-24 12:45:07,949] [INFO] Running command: hmmsearch --tblout GCF_016907925.1_ASM1690792v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference/reference_markers.hmm GCF_016907925.1_ASM1690792v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:08,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:08,357] [INFO] Found 6/6 markers.
[2024-01-24 12:45:08,410] [INFO] Query marker FASTA was written to GCF_016907925.1_ASM1690792v1_genomic.fna/markers.fasta
[2024-01-24 12:45:08,411] [INFO] Task started: Blastn
[2024-01-24 12:45:08,411] [INFO] Running command: blastn -query GCF_016907925.1_ASM1690792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference/reference_markers.fasta -out GCF_016907925.1_ASM1690792v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:09,009] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:09,012] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:09,013] [INFO] Target genome list was writen to GCF_016907925.1_ASM1690792v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:09,026] [INFO] Task started: fastANI
[2024-01-24 12:45:09,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ad21a2-1aef-4862-83bd-92ccd23a6e1a/GCF_016907925.1_ASM1690792v1_genomic.fna.gz --refList GCF_016907925.1_ASM1690792v1_genomic.fna/target_genomes.txt --output GCF_016907925.1_ASM1690792v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:22,497] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:22,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:22,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:22,503] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:22,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:22,503] [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
Herpetosiphon giganteus	strain=DSM 589	GCA_016907925.1	2029754	2029754	type	True	100.0	2005	2011	95	conclusive
Herpetosiphon geysericola	strain=DSM 7119	GCA_001306135.1	70996	70996	type	True	92.9665	1746	2011	95	below_threshold
Herpetosiphon llansteffanensis	strain=CA052B	GCA_003205875.1	2094568	2094568	type	True	92.2252	1725	2011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:22,505] [INFO] DFAST Taxonomy check result was written to GCF_016907925.1_ASM1690792v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:22,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:22,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:22,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference/checkm_data
[2024-01-24 12:45:22,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:22,574] [INFO] Task started: CheckM
[2024-01-24 12:45:22,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907925.1_ASM1690792v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907925.1_ASM1690792v1_genomic.fna/checkm_input GCF_016907925.1_ASM1690792v1_genomic.fna/checkm_result
[2024-01-24 12:46:28,515] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:28,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:28,543] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:28,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:28,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907925.1_ASM1690792v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:28,544] [INFO] Task started: Blastn
[2024-01-24 12:46:28,544] [INFO] Running command: blastn -query GCF_016907925.1_ASM1690792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0b11a4-6c58-4790-bb5d-df7f96abc676/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907925.1_ASM1690792v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:29,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:29,318] [INFO] Selected 9 target genomes.
[2024-01-24 12:46:29,318] [INFO] Target genome list was writen to GCF_016907925.1_ASM1690792v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:29,352] [INFO] Task started: fastANI
[2024-01-24 12:46:29,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ad21a2-1aef-4862-83bd-92ccd23a6e1a/GCF_016907925.1_ASM1690792v1_genomic.fna.gz --refList GCF_016907925.1_ASM1690792v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907925.1_ASM1690792v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:41,862] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:41,873] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:41,873] [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_016907925.1	s__Herpetosiphon giganteus	100.0	2005	2011	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001306135.1	s__Herpetosiphon geysericola	92.9665	1746	2011	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205875.1	s__Herpetosiphon llansteffanensis	92.2359	1724	2011	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000018565.1	s__Herpetosiphon aurantiacus	85.4517	1592	2011	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013813565.1	s__JACCRK01 sp013813565	75.775	93	2011	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__JACCRK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:41,876] [INFO] GTDB search result was written to GCF_016907925.1_ASM1690792v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:41,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:41,880] [INFO] DFAST_QC result json was written to GCF_016907925.1_ASM1690792v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:41,880] [INFO] DFAST_QC completed!
[2024-01-24 12:46:41,881] [INFO] Total running time: 0h1m58s