[2023-07-01 04:06:01,446] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:06:01,449] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:06:01,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference
[2023-07-01 04:06:03,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:06:03,963] [INFO] Task started: Prodigal
[2023-07-01 04:06:03,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgac7616c4-16e5-4b65-8c1b-b0e999cea9b4/GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna.gz | prodigal -d GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/cds.fna -a GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:06:05,577] [INFO] Task succeeded: Prodigal
[2023-07-01 04:06:05,577] [INFO] Task started: HMMsearch
[2023-07-01 04:06:05,578] [INFO] Running command: hmmsearch --tblout GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference/reference_markers.hmm GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:06:05,754] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:06:05,756] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgac7616c4-16e5-4b65-8c1b-b0e999cea9b4/GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna.gz]
[2023-07-01 04:06:05,768] [INFO] Query marker FASTA was written to GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/markers.fasta
[2023-07-01 04:06:05,768] [INFO] Task started: Blastn
[2023-07-01 04:06:05,768] [INFO] Running command: blastn -query GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference/reference_markers.fasta -out GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:06:07,704] [INFO] Task succeeded: Blastn
[2023-07-01 04:06:07,710] [INFO] Selected 7 target genomes.
[2023-07-01 04:06:07,710] [INFO] Target genome list was writen to GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/target_genomes.txt
[2023-07-01 04:06:07,713] [INFO] Task started: fastANI
[2023-07-01 04:06:07,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7616c4-16e5-4b65-8c1b-b0e999cea9b4/GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna.gz --refList GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/target_genomes.txt --output GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:06:09,721] [INFO] Task succeeded: fastANI
[2023-07-01 04:06:09,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:06:09,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:06:09,724] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:06:09,724] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:06:09,724] [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
--------------------------------------------------------------------------------
[2023-07-01 04:06:09,726] [INFO] DFAST Taxonomy check result was written to GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/tc_result.tsv
[2023-07-01 04:06:09,727] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:06:09,727] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:06:09,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference/checkm_data
[2023-07-01 04:06:09,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:06:09,742] [INFO] Task started: CheckM
[2023-07-01 04:06:09,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/checkm_input GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/checkm_result
[2023-07-01 04:06:25,530] [INFO] Task succeeded: CheckM
[2023-07-01 04:06:25,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.55%
Contamintation: 0.90%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 04:06:25,552] [INFO] ===== Completeness check finished =====
[2023-07-01 04:06:25,553] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:06:25,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/markers.fasta)
[2023-07-01 04:06:25,553] [INFO] Task started: Blastn
[2023-07-01 04:06:25,554] [INFO] Running command: blastn -query GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f32bfb7-9151-4efb-99db-b8c5d1e899aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:06:26,021] [INFO] Task succeeded: Blastn
[2023-07-01 04:06:26,025] [INFO] Selected 8 target genomes.
[2023-07-01 04:06:26,025] [INFO] Target genome list was writen to GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:06:26,026] [INFO] Task started: fastANI
[2023-07-01 04:06:26,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7616c4-16e5-4b65-8c1b-b0e999cea9b4/GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna.gz --refList GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/target_genomes_gtdb.txt --output GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:06:27,189] [INFO] Task succeeded: fastANI
[2023-07-01 04:06:27,199] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 04:06:27,199] [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_000419465.1	s__Fonsibacter sp000419465	83.454	53	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882565.1	s__Fonsibacter sp018882565	83.35	62	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	96.85	95.99	0.76	0.70	5	-
GCA_000510845.1	s__Fonsibacter sp000510845	83.0988	54	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.98	95.03	0.69	0.68	4	-
GCA_010021145.1	s__Fonsibacter lacus_A	82.8391	54	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	99.30	99.10	0.81	0.79	3	-
GCA_018658635.1	s__Fonsibacter sp018658635	82.3523	59	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002688585.1	s__Fonsibacter ubiquis	81.5154	69	78	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	97.79	97.41	0.98	0.94	23	-
--------------------------------------------------------------------------------
[2023-07-01 04:06:27,201] [INFO] GTDB search result was written to GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/result_gtdb.tsv
[2023-07-01 04:06:27,202] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:06:27,204] [INFO] DFAST_QC result json was written to GCA_903856515.1_freshwater_MAG_---_LinL5_bin-0142_genomic.fna/dqc_result.json
[2023-07-01 04:06:27,204] [INFO] DFAST_QC completed!
[2023-07-01 04:06:27,205] [INFO] Total running time: 0h0m26s