[2024-01-24 14:39:15,307] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference
[2024-01-24 14:39:16,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,701] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,701] [INFO] Running command: gunzip -c /var/lib/cwl/stgede76533-d12e-4293-b6e1-30984d3e2c1c/GCF_017357525.1_ASM1735752v1_genomic.fna.gz | prodigal -d GCF_017357525.1_ASM1735752v1_genomic.fna/cds.fna -a GCF_017357525.1_ASM1735752v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:25,536] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:25,536] [INFO] Task started: HMMsearch
[2024-01-24 14:39:25,536] [INFO] Running command: hmmsearch --tblout GCF_017357525.1_ASM1735752v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference/reference_markers.hmm GCF_017357525.1_ASM1735752v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:25,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:25,836] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgede76533-d12e-4293-b6e1-30984d3e2c1c/GCF_017357525.1_ASM1735752v1_genomic.fna.gz]
[2024-01-24 14:39:25,869] [INFO] Query marker FASTA was written to GCF_017357525.1_ASM1735752v1_genomic.fna/markers.fasta
[2024-01-24 14:39:25,870] [INFO] Task started: Blastn
[2024-01-24 14:39:25,870] [INFO] Running command: blastn -query GCF_017357525.1_ASM1735752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference/reference_markers.fasta -out GCF_017357525.1_ASM1735752v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:26,407] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:26,411] [INFO] Selected 6 target genomes.
[2024-01-24 14:39:26,411] [INFO] Target genome list was writen to GCF_017357525.1_ASM1735752v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:26,415] [INFO] Task started: fastANI
[2024-01-24 14:39:26,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgede76533-d12e-4293-b6e1-30984d3e2c1c/GCF_017357525.1_ASM1735752v1_genomic.fna.gz --refList GCF_017357525.1_ASM1735752v1_genomic.fna/target_genomes.txt --output GCF_017357525.1_ASM1735752v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:31,112] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:31,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:31,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:31,123] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:31,123] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:31,124] [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
Methanofollis formosanus	strain=ML15	GCA_019633745.1	299308	299308	type	True	89.1819	746	915	95	below_threshold
Methanofollis ethanolicus	strain=HASU	GCA_001571385.1	488124	488124	type	True	80.8479	476	915	95	below_threshold
Methanofollis tationis	strain=DSM 2702	GCA_013377755.1	81417	81417	type	True	79.6494	368	915	95	below_threshold
Methanofollis liminatans	strain=DSM 4140	GCA_000275865.1	2201	2201	type	True	79.5518	396	915	95	below_threshold
Methanofollis fontis	strain=FWC-SCC2	GCA_004297185.1	2052832	2052832	type	True	78.9681	321	915	95	below_threshold
Methanoregula boonei	strain=6A8	GCA_000017625.1	358766	358766	type	True	76.7353	50	915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:31,126] [INFO] DFAST Taxonomy check result was written to GCF_017357525.1_ASM1735752v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:31,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:31,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:31,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference/checkm_data
[2024-01-24 14:39:31,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:31,164] [INFO] Task started: CheckM
[2024-01-24 14:39:31,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017357525.1_ASM1735752v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017357525.1_ASM1735752v1_genomic.fna/checkm_input GCF_017357525.1_ASM1735752v1_genomic.fna/checkm_result
[2024-01-24 14:40:02,210] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:02,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:02,258] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:02,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:02,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017357525.1_ASM1735752v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:02,259] [INFO] Task started: Blastn
[2024-01-24 14:40:02,259] [INFO] Running command: blastn -query GCF_017357525.1_ASM1735752v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b78b3c-21f6-4129-aa93-03c67cf485b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017357525.1_ASM1735752v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:02,829] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:02,832] [INFO] Selected 6 target genomes.
[2024-01-24 14:40:02,833] [INFO] Target genome list was writen to GCF_017357525.1_ASM1735752v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:02,838] [INFO] Task started: fastANI
[2024-01-24 14:40:02,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgede76533-d12e-4293-b6e1-30984d3e2c1c/GCF_017357525.1_ASM1735752v1_genomic.fna.gz --refList GCF_017357525.1_ASM1735752v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017357525.1_ASM1735752v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:06,825] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:06,832] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:40:06,833] [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_017875325.1	s__Methanofollis sp017875325	85.9877	696	915	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498315.1	s__Methanofollis sp002498315	81.1992	474	915	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571385.1	s__Methanofollis ethanolicus	80.8337	475	915	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377755.1	s__Methanofollis tationis	79.6294	369	915	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275865.1	s__Methanofollis liminatans	79.5589	395	915	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004297185.1	s__Methanofollis sp004297185	78.982	320	915	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:06,836] [INFO] GTDB search result was written to GCF_017357525.1_ASM1735752v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:06,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:06,839] [INFO] DFAST_QC result json was written to GCF_017357525.1_ASM1735752v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:06,840] [INFO] DFAST_QC completed!
[2024-01-24 14:40:06,840] [INFO] Total running time: 0h0m52s