[2023-06-28 19:04:25,592] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:04:25,594] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:04:25,594] [INFO] DQC Reference Directory: /var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference
[2023-06-28 19:04:26,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:04:26,970] [INFO] Task started: Prodigal
[2023-06-28 19:04:26,970] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6cb4e07-c7d8-4f90-a540-965c2cb27b76/GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:04:36,025] [INFO] Task succeeded: Prodigal
[2023-06-28 19:04:36,025] [INFO] Task started: HMMsearch
[2023-06-28 19:04:36,025] [INFO] Running command: hmmsearch --tblout GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference/reference_markers.hmm GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:04:36,250] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:04:36,251] [INFO] Found 6/6 markers.
[2023-06-28 19:04:36,272] [INFO] Query marker FASTA was written to GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 19:04:36,272] [INFO] Task started: Blastn
[2023-06-28 19:04:36,272] [INFO] Running command: blastn -query GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference/reference_markers.fasta -out GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:36,867] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:36,871] [INFO] Selected 26 target genomes.
[2023-06-28 19:04:36,871] [INFO] Target genome list was writen to GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 19:04:36,893] [INFO] Task started: fastANI
[2023-06-28 19:04:36,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6cb4e07-c7d8-4f90-a540-965c2cb27b76/GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:52,918] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:52,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:52,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:52,921] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:04:52,921] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:04:52,921] [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
--------------------------------------------------------------------------------
[2023-06-28 19:04:52,924] [INFO] DFAST Taxonomy check result was written to GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 19:04:52,924] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:52,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:52,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference/checkm_data
[2023-06-28 19:04:52,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:52,953] [INFO] Task started: CheckM
[2023-06-28 19:04:52,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 19:05:23,696] [INFO] Task succeeded: CheckM
[2023-06-28 19:05:23,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:05:23,715] [INFO] ===== Completeness check finished =====
[2023-06-28 19:05:23,715] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:05:23,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 19:05:23,716] [INFO] Task started: Blastn
[2023-06-28 19:05:23,716] [INFO] Running command: blastn -query GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg89ff05ed-c7d2-4b8a-b3ff-92160ece2bfb/dqc_reference/reference_markers_gtdb.fasta -out GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:05:24,482] [INFO] Task succeeded: Blastn
[2023-06-28 19:05:24,487] [INFO] Selected 16 target genomes.
[2023-06-28 19:05:24,487] [INFO] Target genome list was writen to GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:05:24,544] [INFO] Task started: fastANI
[2023-06-28 19:05:24,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6cb4e07-c7d8-4f90-a540-965c2cb27b76/GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:05:30,883] [INFO] Task succeeded: fastANI
[2023-06-28 19:05:30,900] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:05:30,901] [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_003445735.1	s__UBA10364 sp003445735	97.6687	363	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	conclusive
GCA_003455605.1	s__UBA10364 sp003455605	93.1347	270	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378005.1	s__UBA10364 sp002378005	86.7009	440	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.86	99.85	0.95	0.94	3	-
GCA_003545085.1	s__UBA10364 sp003545085	81.5726	115	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	80.4686	139	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	80.4101	145	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_012269745.1	s__UBA10364 sp012269745	79.8941	132	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911625.1	s__UBA10364 sp013911625	79.7907	74	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430755.1	s__UBA10364 sp002430755	79.4359	116	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	78.3641	95	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023665.1	s__UBA10364 sp003023665	77.6408	58	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.70	98.70	0.79	0.79	2	-
GCA_002707525.1	s__UBA10364 sp002707525	76.881	59	530	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:05:30,903] [INFO] GTDB search result was written to GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 19:05:30,903] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:05:30,906] [INFO] DFAST_QC result json was written to GCA_913051565.1_ERR599029_bin.48_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 19:05:30,906] [INFO] DFAST_QC completed!
[2023-06-28 19:05:30,906] [INFO] Total running time: 0h1m5s