[2024-01-24 12:14:33,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference
[2024-01-24 12:14:35,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,151] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg8292bc89-4184-4003-8663-75ce4801ebee/GCF_019633745.1_ASM1963374v1_genomic.fna.gz | prodigal -d GCF_019633745.1_ASM1963374v1_genomic.fna/cds.fna -a GCF_019633745.1_ASM1963374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:42,591] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:42,592] [INFO] Task started: HMMsearch
[2024-01-24 12:14:42,592] [INFO] Running command: hmmsearch --tblout GCF_019633745.1_ASM1963374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference/reference_markers.hmm GCF_019633745.1_ASM1963374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:42,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:42,768] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8292bc89-4184-4003-8663-75ce4801ebee/GCF_019633745.1_ASM1963374v1_genomic.fna.gz]
[2024-01-24 12:14:42,805] [INFO] Query marker FASTA was written to GCF_019633745.1_ASM1963374v1_genomic.fna/markers.fasta
[2024-01-24 12:14:42,805] [INFO] Task started: Blastn
[2024-01-24 12:14:42,805] [INFO] Running command: blastn -query GCF_019633745.1_ASM1963374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference/reference_markers.fasta -out GCF_019633745.1_ASM1963374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:43,261] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:43,264] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:43,264] [INFO] Target genome list was writen to GCF_019633745.1_ASM1963374v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:43,267] [INFO] Task started: fastANI
[2024-01-24 12:14:43,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg8292bc89-4184-4003-8663-75ce4801ebee/GCF_019633745.1_ASM1963374v1_genomic.fna.gz --refList GCF_019633745.1_ASM1963374v1_genomic.fna/target_genomes.txt --output GCF_019633745.1_ASM1963374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:49,616] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:49,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:49,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:49,657] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:49,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:49,658] [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	100.0	988	988	95	conclusive
Methanofollis ethanolicus	strain=HASU	GCA_001571385.1	488124	488124	type	True	80.9425	511	988	95	below_threshold
Methanofollis tationis	strain=DSM 2702	GCA_013377755.1	81417	81417	type	True	80.0463	392	988	95	below_threshold
Methanofollis liminatans	strain=DSM 4140	GCA_000275865.1	2201	2201	type	True	79.895	435	988	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	77.4764	177	988	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	77.4303	178	988	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	77.3995	180	988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:49,659] [INFO] DFAST Taxonomy check result was written to GCF_019633745.1_ASM1963374v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:49,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:49,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:49,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference/checkm_data
[2024-01-24 12:14:49,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:49,696] [INFO] Task started: CheckM
[2024-01-24 12:14:49,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019633745.1_ASM1963374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019633745.1_ASM1963374v1_genomic.fna/checkm_input GCF_019633745.1_ASM1963374v1_genomic.fna/checkm_result
[2024-01-24 12:15:18,512] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:18,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:18,527] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:18,527] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:18,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019633745.1_ASM1963374v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:18,528] [INFO] Task started: Blastn
[2024-01-24 12:15:18,528] [INFO] Running command: blastn -query GCF_019633745.1_ASM1963374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79ccc257-4b2d-4aba-9c17-ae9bbe6c8016/dqc_reference/reference_markers_gtdb.fasta -out GCF_019633745.1_ASM1963374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,306] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,309] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:19,309] [INFO] Target genome list was writen to GCF_019633745.1_ASM1963374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:19,313] [INFO] Task started: fastANI
[2024-01-24 12:15:19,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg8292bc89-4184-4003-8663-75ce4801ebee/GCF_019633745.1_ASM1963374v1_genomic.fna.gz --refList GCF_019633745.1_ASM1963374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019633745.1_ASM1963374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:23,768] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:23,785] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:23,785] [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	86.1416	697	988	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	80.9211	512	988	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	80.8344	491	988	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	80.0325	393	988	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	79.871	437	988	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanofollaceae;g__Methanofollis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602375.1	s__Methanoculleus horonobensis	77.4496	176	988	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017125.1	s__Methanoculleus sediminis	77.416	179	988	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,787] [INFO] GTDB search result was written to GCF_019633745.1_ASM1963374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:23,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:23,789] [INFO] DFAST_QC result json was written to GCF_019633745.1_ASM1963374v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:23,790] [INFO] DFAST_QC completed!
[2024-01-24 12:15:23,790] [INFO] Total running time: 0h0m50s