[2023-06-07 19:48:11,806] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:48:11,811] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:48:11,811] [INFO] DQC Reference Directory: /var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference
[2023-06-07 19:48:13,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:48:13,870] [INFO] Task started: Prodigal
[2023-06-07 19:48:13,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg25273f15-b4b6-4bac-adf3-722f6313046e/GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:48:15,589] [INFO] Task succeeded: Prodigal
[2023-06-07 19:48:15,590] [INFO] Task started: HMMsearch
[2023-06-07 19:48:15,590] [INFO] Running command: hmmsearch --tblout GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference/reference_markers.hmm GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:48:15,817] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:48:15,819] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg25273f15-b4b6-4bac-adf3-722f6313046e/GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 19:48:15,846] [INFO] Query marker FASTA was written to GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 19:48:15,846] [INFO] Task started: Blastn
[2023-06-07 19:48:15,846] [INFO] Running command: blastn -query GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference/reference_markers.fasta -out GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:48:17,678] [INFO] Task succeeded: Blastn
[2023-06-07 19:48:17,683] [INFO] Selected 6 target genomes.
[2023-06-07 19:48:17,684] [INFO] Target genome list was writen to GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 19:48:17,685] [INFO] Task started: fastANI
[2023-06-07 19:48:17,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg25273f15-b4b6-4bac-adf3-722f6313046e/GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:48:20,100] [INFO] Task succeeded: fastANI
[2023-06-07 19:48:20,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:48:20,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:48:20,109] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:48:20,109] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 19:48:20,109] [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 gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	84.649	232	255	95	below_threshold
Methanobrevibacter oralis	strain=DSM 7256	GCA_001639275.1	66851	66851	type	True	80.0451	166	255	95	below_threshold
Methanobrevibacter smithii	strain=ATCC 35061; PS; DSMZ 861	GCA_000016525.1	2173	2173	type	True	79.635	161	255	95	below_threshold
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	79.5659	146	255	95	below_threshold
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	77.7622	82	255	95	below_threshold
Methanobrevibacter arboriphilus	strain=DH1	GCA_002072215.1	39441	39441	type	True	76.6851	51	255	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 19:48:20,115] [INFO] DFAST Taxonomy check result was written to GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 19:48:20,115] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:48:20,115] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:48:20,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference/checkm_data
[2023-06-07 19:48:20,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:48:20,144] [INFO] Task started: CheckM
[2023-06-07 19:48:20,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 19:48:35,213] [INFO] Task succeeded: CheckM
[2023-06-07 19:48:35,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:48:35,233] [INFO] ===== Completeness check finished =====
[2023-06-07 19:48:35,233] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:48:35,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 19:48:35,234] [INFO] Task started: Blastn
[2023-06-07 19:48:35,234] [INFO] Running command: blastn -query GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13bebe9-272e-4c6c-b874-d8adc2496e68/dqc_reference/reference_markers_gtdb.fasta -out GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:48:35,775] [INFO] Task succeeded: Blastn
[2023-06-07 19:48:35,779] [INFO] Selected 6 target genomes.
[2023-06-07 19:48:35,780] [INFO] Target genome list was writen to GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:48:35,781] [INFO] Task started: fastANI
[2023-06-07 19:48:35,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg25273f15-b4b6-4bac-adf3-722f6313046e/GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:48:37,762] [INFO] Task succeeded: fastANI
[2023-06-07 19:48:37,769] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 19:48:37,770] [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_900769095.1	s__Methanobrevibacter_A sp900769095	98.1911	198	255	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.12	98.84	0.74	0.68	3	conclusive
GCF_003814835.1	s__Methanobrevibacter_A gottschalkii	84.649	232	255	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.46	98.93	0.95	0.91	3	-
GCA_902785855.1	s__Methanobrevibacter_A sp902785855	81.7851	185	255	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.27	97.27	0.75	0.75	2	-
GCA_902770715.1	s__Methanobrevibacter_A sp902770715	81.7719	177	255	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.49	97.18	0.82	0.81	3	-
GCA_904501935.1	s__Methanobrevibacter_A sp904501935	81.3087	158	255	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017539065.1	s__Methanobrevibacter_A sp017539065	81.0162	179	255	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:48:37,772] [INFO] GTDB search result was written to GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 19:48:37,772] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:48:37,775] [INFO] DFAST_QC result json was written to GCA_945971405.1_SRR15725431_bin.33_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 19:48:37,775] [INFO] DFAST_QC completed!
[2023-06-07 19:48:37,775] [INFO] Total running time: 0h0m26s