[2023-06-29 21:20:04,617] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:20:04,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:20:04,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference
[2023-06-29 21:20:05,933] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:20:05,934] [INFO] Task started: Prodigal
[2023-06-29 21:20:05,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a535e8f-408d-44a6-9c78-3fd2c9bff65e/GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna.gz | prodigal -d GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/cds.fna -a GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:20:20,408] [INFO] Task succeeded: Prodigal
[2023-06-29 21:20:20,408] [INFO] Task started: HMMsearch
[2023-06-29 21:20:20,408] [INFO] Running command: hmmsearch --tblout GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference/reference_markers.hmm GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:20:20,695] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:20:20,697] [INFO] Found 6/6 markers.
[2023-06-29 21:20:20,731] [INFO] Query marker FASTA was written to GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/markers.fasta
[2023-06-29 21:20:20,731] [INFO] Task started: Blastn
[2023-06-29 21:20:20,731] [INFO] Running command: blastn -query GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/markers.fasta -db /var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference/reference_markers.fasta -out GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:20:21,321] [INFO] Task succeeded: Blastn
[2023-06-29 21:20:21,325] [INFO] Selected 30 target genomes.
[2023-06-29 21:20:21,326] [INFO] Target genome list was writen to GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/target_genomes.txt
[2023-06-29 21:20:21,327] [INFO] Task started: fastANI
[2023-06-29 21:20:21,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a535e8f-408d-44a6-9c78-3fd2c9bff65e/GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna.gz --refList GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/target_genomes.txt --output GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:20:38,685] [INFO] Task succeeded: fastANI
[2023-06-29 21:20:38,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:20:38,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:20:38,688] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:20:38,688] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:20:38,688] [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
--------------------------------------------------------------------------------
[2023-06-29 21:20:38,691] [INFO] DFAST Taxonomy check result was written to GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/tc_result.tsv
[2023-06-29 21:20:38,692] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:20:38,692] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:20:38,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference/checkm_data
[2023-06-29 21:20:38,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:20:38,735] [INFO] Task started: CheckM
[2023-06-29 21:20:38,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/checkm_input GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/checkm_result
[2023-06-29 21:21:23,060] [INFO] Task succeeded: CheckM
[2023-06-29 21:21:23,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.30%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:21:23,084] [INFO] ===== Completeness check finished =====
[2023-06-29 21:21:23,084] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:21:23,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/markers.fasta)
[2023-06-29 21:21:23,085] [INFO] Task started: Blastn
[2023-06-29 21:21:23,085] [INFO] Running command: blastn -query GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/markers.fasta -db /var/lib/cwl/stg074c21cc-2c69-4549-a980-af86e5255b8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:21:23,854] [INFO] Task succeeded: Blastn
[2023-06-29 21:21:23,859] [INFO] Selected 24 target genomes.
[2023-06-29 21:21:23,860] [INFO] Target genome list was writen to GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:21:23,873] [INFO] Task started: fastANI
[2023-06-29 21:21:23,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a535e8f-408d-44a6-9c78-3fd2c9bff65e/GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna.gz --refList GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/target_genomes_gtdb.txt --output GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:21:36,963] [INFO] Task succeeded: fastANI
[2023-06-29 21:21:36,977] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:21:36,978] [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_903911435.1	s__2-12-FULL-35-15 sp903911435	99.6761	743	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.39	97.58	0.90	0.87	8	conclusive
GCA_903926385.1	s__2-12-FULL-35-15 sp903926385	82.1723	228	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.98	99.96	0.98	0.98	5	-
GCA_903870175.1	s__2-12-FULL-35-15 sp903870175	77.5096	161	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.44	99.36	0.89	0.82	6	-
GCA_903881065.1	s__2-12-FULL-35-15 sp903881065	77.3754	154	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787165.1	s__JAEUTT01 sp016787165	77.1061	51	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722565.1	s__2-12-FULL-35-15 sp016722565	76.5867	84	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919535.1	s__2-12-FULL-35-15 sp903919535	76.4984	90	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.81	99.81	0.93	0.93	2	-
GCA_016707685.1	s__JAEUTT01 sp016707685	76.4474	78	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769385.1	s__2-12-FULL-35-15 sp001769385	76.414	85	795	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:21:36,980] [INFO] GTDB search result was written to GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/result_gtdb.tsv
[2023-06-29 21:21:36,980] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:21:36,983] [INFO] DFAST_QC result json was written to GCA_903874635.1_freshwater_MAG_---_Ja1-D4_bin-199_genomic.fna/dqc_result.json
[2023-06-29 21:21:36,984] [INFO] DFAST_QC completed!
[2023-06-29 21:21:36,984] [INFO] Total running time: 0h1m32s