[2023-06-29 21:28:34,895] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:28:34,897] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:28:34,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference
[2023-06-29 21:28:36,039] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:28:36,040] [INFO] Task started: Prodigal
[2023-06-29 21:28:36,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg60e73adb-0932-40a1-8028-20206e14b1d6/GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna.gz | prodigal -d GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/cds.fna -a GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:28:39,915] [INFO] Task succeeded: Prodigal
[2023-06-29 21:28:39,915] [INFO] Task started: HMMsearch
[2023-06-29 21:28:39,915] [INFO] Running command: hmmsearch --tblout GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference/reference_markers.hmm GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:28:40,089] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:28:40,090] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60e73adb-0932-40a1-8028-20206e14b1d6/GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna.gz]
[2023-06-29 21:28:40,113] [INFO] Query marker FASTA was written to GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/markers.fasta
[2023-06-29 21:28:40,113] [INFO] Task started: Blastn
[2023-06-29 21:28:40,113] [INFO] Running command: blastn -query GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/markers.fasta -db /var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference/reference_markers.fasta -out GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:40,697] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:40,702] [INFO] Selected 25 target genomes.
[2023-06-29 21:28:40,703] [INFO] Target genome list was writen to GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/target_genomes.txt
[2023-06-29 21:28:40,708] [INFO] Task started: fastANI
[2023-06-29 21:28:40,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e73adb-0932-40a1-8028-20206e14b1d6/GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna.gz --refList GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/target_genomes.txt --output GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:28:56,240] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:56,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:28:56,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:28:56,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:28:56,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:28:56,242] [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 21:28:56,244] [INFO] DFAST Taxonomy check result was written to GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/tc_result.tsv
[2023-06-29 21:28:56,245] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:28:56,245] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:28:56,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference/checkm_data
[2023-06-29 21:28:56,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:28:56,269] [INFO] Task started: CheckM
[2023-06-29 21:28:56,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/checkm_input GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/checkm_result
[2023-06-29 21:29:16,160] [INFO] Task succeeded: CheckM
[2023-06-29 21:29:16,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.78%
Contamintation: 3.94%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-29 21:29:16,207] [INFO] ===== Completeness check finished =====
[2023-06-29 21:29:16,207] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:29:16,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/markers.fasta)
[2023-06-29 21:29:16,207] [INFO] Task started: Blastn
[2023-06-29 21:29:16,208] [INFO] Running command: blastn -query GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/markers.fasta -db /var/lib/cwl/stgfed98328-bfb1-4d71-8bd3-a8a1af844100/dqc_reference/reference_markers_gtdb.fasta -out GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:29:17,015] [INFO] Task succeeded: Blastn
[2023-06-29 21:29:17,019] [INFO] Selected 15 target genomes.
[2023-06-29 21:29:17,019] [INFO] Target genome list was writen to GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:29:17,076] [INFO] Task started: fastANI
[2023-06-29 21:29:17,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e73adb-0932-40a1-8028-20206e14b1d6/GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna.gz --refList GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/target_genomes_gtdb.txt --output GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:29:24,556] [INFO] Task succeeded: fastANI
[2023-06-29 21:29:24,560] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:29:24,560] [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_903835265.1	s__UBA6136 sp903835265	99.5512	281	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__UBA6136	95.0	99.80	99.80	0.92	0.92	2	conclusive
GCA_009922685.1	s__UBA6136 sp009922685	90.4197	273	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__UBA6136	95.0	99.51	99.31	0.92	0.89	6	-
GCA_007280285.1	s__UBA6136 sp007280285	84.8916	254	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__UBA6136	95.0	98.33	98.09	0.85	0.81	13	-
--------------------------------------------------------------------------------
[2023-06-29 21:29:24,564] [INFO] GTDB search result was written to GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/result_gtdb.tsv
[2023-06-29 21:29:24,565] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:29:24,567] [INFO] DFAST_QC result json was written to GCA_903867145.1_freshwater_MAG_---_Umea1p1_bin-819_genomic.fna/dqc_result.json
[2023-06-29 21:29:24,568] [INFO] DFAST_QC completed!
[2023-06-29 21:29:24,568] [INFO] Total running time: 0h0m50s