[2023-06-28 07:11:29,036] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:11:29,040] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:11:29,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference
[2023-06-28 07:11:31,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:11:31,498] [INFO] Task started: Prodigal
[2023-06-28 07:11:31,498] [INFO] Running command: gunzip -c /var/lib/cwl/stgc76e0495-95e1-43e5-ad4c-772316a0cf26/GCA_017410345.1_ASM1741034v1_genomic.fna.gz | prodigal -d GCA_017410345.1_ASM1741034v1_genomic.fna/cds.fna -a GCA_017410345.1_ASM1741034v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:11:35,276] [INFO] Task succeeded: Prodigal
[2023-06-28 07:11:35,277] [INFO] Task started: HMMsearch
[2023-06-28 07:11:35,277] [INFO] Running command: hmmsearch --tblout GCA_017410345.1_ASM1741034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference/reference_markers.hmm GCA_017410345.1_ASM1741034v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:11:35,474] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:11:35,476] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc76e0495-95e1-43e5-ad4c-772316a0cf26/GCA_017410345.1_ASM1741034v1_genomic.fna.gz]
[2023-06-28 07:11:35,510] [INFO] Query marker FASTA was written to GCA_017410345.1_ASM1741034v1_genomic.fna/markers.fasta
[2023-06-28 07:11:35,511] [INFO] Task started: Blastn
[2023-06-28 07:11:35,511] [INFO] Running command: blastn -query GCA_017410345.1_ASM1741034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference/reference_markers.fasta -out GCA_017410345.1_ASM1741034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:11:36,012] [INFO] Task succeeded: Blastn
[2023-06-28 07:11:36,017] [INFO] Selected 5 target genomes.
[2023-06-28 07:11:36,017] [INFO] Target genome list was writen to GCA_017410345.1_ASM1741034v1_genomic.fna/target_genomes.txt
[2023-06-28 07:11:36,019] [INFO] Task started: fastANI
[2023-06-28 07:11:36,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgc76e0495-95e1-43e5-ad4c-772316a0cf26/GCA_017410345.1_ASM1741034v1_genomic.fna.gz --refList GCA_017410345.1_ASM1741034v1_genomic.fna/target_genomes.txt --output GCA_017410345.1_ASM1741034v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:11:38,134] [INFO] Task succeeded: fastANI
[2023-06-28 07:11:38,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:11:38,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:11:38,146] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:11:38,146] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 07:11:38,146] [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
Methanobrevibacter ruminantium	strain=M1	GCA_000024185.1	83816	83816	type	True	81.4545	380	581	95	below_threshold
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	81.3293	376	581	95	below_threshold
Methanobrevibacter filiformis	strain=DSM 11501	GCA_001639265.1	55758	55758	type	True	76.3771	56	581	95	below_threshold
Methanobrevibacter boviskoreani	strain=JH1	GCA_000320505.2	1348249	1348249	type	True	76.3373	82	581	95	below_threshold
Methanobrevibacter wolinii	strain=SH	GCA_000621965.1	190977	190977	type	True	76.2051	99	581	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:11:38,148] [INFO] DFAST Taxonomy check result was written to GCA_017410345.1_ASM1741034v1_genomic.fna/tc_result.tsv
[2023-06-28 07:11:38,149] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:11:38,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:11:38,149] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference/checkm_data
[2023-06-28 07:11:38,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:11:38,175] [INFO] Task started: CheckM
[2023-06-28 07:11:38,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017410345.1_ASM1741034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017410345.1_ASM1741034v1_genomic.fna/checkm_input GCA_017410345.1_ASM1741034v1_genomic.fna/checkm_result
[2023-06-28 07:11:59,863] [INFO] Task succeeded: CheckM
[2023-06-28 07:11:59,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:11:59,886] [INFO] ===== Completeness check finished =====
[2023-06-28 07:11:59,887] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:11:59,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017410345.1_ASM1741034v1_genomic.fna/markers.fasta)
[2023-06-28 07:11:59,888] [INFO] Task started: Blastn
[2023-06-28 07:11:59,888] [INFO] Running command: blastn -query GCA_017410345.1_ASM1741034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4075c40f-52c4-4c55-ad86-77f42574a4b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_017410345.1_ASM1741034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:12:00,437] [INFO] Task succeeded: Blastn
[2023-06-28 07:12:00,442] [INFO] Selected 8 target genomes.
[2023-06-28 07:12:00,442] [INFO] Target genome list was writen to GCA_017410345.1_ASM1741034v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:12:00,446] [INFO] Task started: fastANI
[2023-06-28 07:12:00,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgc76e0495-95e1-43e5-ad4c-772316a0cf26/GCA_017410345.1_ASM1741034v1_genomic.fna.gz --refList GCA_017410345.1_ASM1741034v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017410345.1_ASM1741034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:12:04,490] [INFO] Task succeeded: fastANI
[2023-06-28 07:12:04,501] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 07:12:04,501] [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
GCA_017410345.1	s__Methanobrevibacter sp017410345	100.0	576	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902784195.1	s__Methanobrevibacter sp902784195	86.0775	485	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	98.44	98.21	0.91	0.88	7	-
GCA_017432245.1	s__Methanobrevibacter sp017432245	85.7588	419	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017646885.1	s__Methanobrevibacter sp017646885	85.7267	204	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063035.1	s__Methanobrevibacter olleyae_A	85.6852	481	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404125.1	s__Methanobrevibacter sp017404125	85.2715	262	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017652345.1	s__Methanobrevibacter sp017652345	85.1967	140	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769175.1	s__Methanobrevibacter sp902769175	82.911	432	581	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:12:04,503] [INFO] GTDB search result was written to GCA_017410345.1_ASM1741034v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:12:04,504] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:12:04,506] [INFO] DFAST_QC result json was written to GCA_017410345.1_ASM1741034v1_genomic.fna/dqc_result.json
[2023-06-28 07:12:04,507] [INFO] DFAST_QC completed!
[2023-06-28 07:12:04,507] [INFO] Total running time: 0h0m35s