[2024-01-24 13:49:27,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference
[2024-01-24 13:49:28,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,830] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg937bd41b-a751-465d-bf7a-1d158a4ee737/GCF_004137855.1_ASM413785v1_genomic.fna.gz | prodigal -d GCF_004137855.1_ASM413785v1_genomic.fna/cds.fna -a GCF_004137855.1_ASM413785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:33,638] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:33,639] [INFO] Task started: HMMsearch
[2024-01-24 13:49:33,639] [INFO] Running command: hmmsearch --tblout GCF_004137855.1_ASM413785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference/reference_markers.hmm GCF_004137855.1_ASM413785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:33,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:33,896] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg937bd41b-a751-465d-bf7a-1d158a4ee737/GCF_004137855.1_ASM413785v1_genomic.fna.gz]
[2024-01-24 13:49:33,922] [INFO] Query marker FASTA was written to GCF_004137855.1_ASM413785v1_genomic.fna/markers.fasta
[2024-01-24 13:49:33,923] [INFO] Task started: Blastn
[2024-01-24 13:49:33,923] [INFO] Running command: blastn -query GCF_004137855.1_ASM413785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference/reference_markers.fasta -out GCF_004137855.1_ASM413785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,472] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,475] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:34,475] [INFO] Target genome list was writen to GCF_004137855.1_ASM413785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:34,481] [INFO] Task started: fastANI
[2024-01-24 13:49:34,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg937bd41b-a751-465d-bf7a-1d158a4ee737/GCF_004137855.1_ASM413785v1_genomic.fna.gz --refList GCF_004137855.1_ASM413785v1_genomic.fna/target_genomes.txt --output GCF_004137855.1_ASM413785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:38,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:38,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:38,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:38,129] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:38,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:38,130] [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
Methanohalophilus profundi	strain=SLHTYRO	GCA_004137855.1	2138083	2138083	type	True	100.0	608	608	95	conclusive
Methanohalophilus portucalensis	strain=FDF-1	GCA_001888095.1	39664	39664	type	True	94.4784	523	608	95	below_threshold
Methanohalophilus portucalensis	strain=DSM 7471	GCA_003722115.1	39664	39664	type	True	94.4478	531	608	95	below_threshold
Methanohalophilus portucalensis	strain=FDF-1T	GCA_002761295.1	39664	39664	type	True	94.4165	537	608	95	below_threshold
Methanohalophilus portucalensis	strain=FDF-1	GCA_900177455.1	39664	39664	type	True	94.4031	534	608	95	below_threshold
Methanohalophilus halophilus	strain=Z-7982	GCA_001889405.1	2177	2177	type	True	92.7254	522	608	95	below_threshold
Methanohalophilus halophilus	strain=DSM 3094	GCA_003722055.1	2177	2177	type	True	92.7026	523	608	95	below_threshold
Methanohalophilus halophilus	strain=Z-7982	GCA_900106905.1	2177	2177	type	True	92.6821	520	608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:38,132] [INFO] DFAST Taxonomy check result was written to GCF_004137855.1_ASM413785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:38,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:38,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:38,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference/checkm_data
[2024-01-24 13:49:38,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:38,162] [INFO] Task started: CheckM
[2024-01-24 13:49:38,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137855.1_ASM413785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137855.1_ASM413785v1_genomic.fna/checkm_input GCF_004137855.1_ASM413785v1_genomic.fna/checkm_result
[2024-01-24 13:50:00,185] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:00,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,212] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:00,213] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:00,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137855.1_ASM413785v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:00,214] [INFO] Task started: Blastn
[2024-01-24 13:50:00,214] [INFO] Running command: blastn -query GCF_004137855.1_ASM413785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ff576b-682b-4148-8093-45b30e44234e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137855.1_ASM413785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:00,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:00,863] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:00,863] [INFO] Target genome list was writen to GCF_004137855.1_ASM413785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:00,868] [INFO] Task started: fastANI
[2024-01-24 13:50:00,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg937bd41b-a751-465d-bf7a-1d158a4ee737/GCF_004137855.1_ASM413785v1_genomic.fna.gz --refList GCF_004137855.1_ASM413785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137855.1_ASM413785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:04,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,039] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:04,039] [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_004137855.1	s__Methanohalophilus profundi	100.0	608	608	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002761295.1	s__Methanohalophilus portucalensis	94.4178	536	608	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_003722075.1	s__Methanohalophilus sp003722075	93.4449	518	608	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215215.1	s__Methanohalophilus euhalobius	93.1338	501	608	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	99.01	98.21	0.93	0.87	10	-
GCF_001889405.1	s__Methanohalophilus halophilus	92.7254	522	608	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000025865.1	s__Methanohalophilus mahii	91.4712	521	608	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,041] [INFO] GTDB search result was written to GCF_004137855.1_ASM413785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:04,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:04,048] [INFO] DFAST_QC result json was written to GCF_004137855.1_ASM413785v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:04,048] [INFO] DFAST_QC completed!
[2024-01-24 13:50:04,048] [INFO] Total running time: 0h0m37s