[2023-06-13 10:49:43,211] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:43,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:43,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference
[2023-06-13 10:49:44,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:44,460] [INFO] Task started: Prodigal
[2023-06-13 10:49:44,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg6526959f-57c1-44d3-88fb-a0e967b9802b/GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna.gz | prodigal -d GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/cds.fna -a GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:49:47,106] [INFO] Task succeeded: Prodigal
[2023-06-13 10:49:47,106] [INFO] Task started: HMMsearch
[2023-06-13 10:49:47,107] [INFO] Running command: hmmsearch --tblout GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference/reference_markers.hmm GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:49:47,355] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:49:47,357] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6526959f-57c1-44d3-88fb-a0e967b9802b/GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna.gz]
[2023-06-13 10:49:47,381] [INFO] Query marker FASTA was written to GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/markers.fasta
[2023-06-13 10:49:47,381] [INFO] Task started: Blastn
[2023-06-13 10:49:47,382] [INFO] Running command: blastn -query GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference/reference_markers.fasta -out GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:49:47,868] [INFO] Task succeeded: Blastn
[2023-06-13 10:49:47,872] [INFO] Selected 5 target genomes.
[2023-06-13 10:49:47,872] [INFO] Target genome list was writen to GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/target_genomes.txt
[2023-06-13 10:49:47,874] [INFO] Task started: fastANI
[2023-06-13 10:49:47,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg6526959f-57c1-44d3-88fb-a0e967b9802b/GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna.gz --refList GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/target_genomes.txt --output GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:49:49,386] [INFO] Task succeeded: fastANI
[2023-06-13 10:49:49,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:49:49,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:49:49,388] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:49:49,389] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:49:49,389] [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
--------------------------------------------------------------------------------
[2023-06-13 10:49:49,391] [INFO] DFAST Taxonomy check result was written to GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/tc_result.tsv
[2023-06-13 10:49:49,392] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:49:49,392] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:49:49,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference/checkm_data
[2023-06-13 10:49:49,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:49:49,416] [INFO] Task started: CheckM
[2023-06-13 10:49:49,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/checkm_input GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/checkm_result
[2023-06-13 10:50:05,379] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:05,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:05,407] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:05,407] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:05,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/markers.fasta)
[2023-06-13 10:50:05,408] [INFO] Task started: Blastn
[2023-06-13 10:50:05,408] [INFO] Running command: blastn -query GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg340e3227-1ac4-4830-a7cb-1e3eefc2e88e/dqc_reference/reference_markers_gtdb.fasta -out GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:05,852] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:05,856] [INFO] Selected 8 target genomes.
[2023-06-13 10:50:05,856] [INFO] Target genome list was writen to GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:05,863] [INFO] Task started: fastANI
[2023-06-13 10:50:05,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg6526959f-57c1-44d3-88fb-a0e967b9802b/GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna.gz --refList GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:08,431] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:08,439] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:50:08,439] [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_002498985.1	s__MGIIb-O2 sp002498985	95.262	334	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.30	95.20	0.78	0.62	4	conclusive
GCA_002685315.1	s__MGIIb-O2 sp002685315	93.322	256	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495525.1	s__MGIIb-O2 sp002495525	87.2638	361	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	96.68	0.79	0.75	3	-
GCA_902593945.1	s__MGIIb-O2 sp902593945	83.2483	293	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497245.1	s__MGIIb-O2 sp002497245	82.6882	353	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	-
GCA_002504905.1	s__MGIIb-O2 sp002504905	82.0028	349	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
GCA_002686525.1	s__MGIIb-O2 sp002686525	79.9597	265	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.02	96.68	0.82	0.74	10	-
GCA_016777225.1	s__MGIIb-O2 sp016777225	78.908	219	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:08,442] [INFO] GTDB search result was written to GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:08,443] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:08,446] [INFO] DFAST_QC result json was written to GCA_938040705.1_S1_Bin_METABAT_258_1_genomic.fna/dqc_result.json
[2023-06-13 10:50:08,446] [INFO] DFAST_QC completed!
[2023-06-13 10:50:08,446] [INFO] Total running time: 0h0m25s