[2023-06-17 15:46:53,457] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:46:53,459] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:46:53,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference
[2023-06-17 15:46:55,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:46:55,477] [INFO] Task started: Prodigal
[2023-06-17 15:46:55,477] [INFO] Running command: gunzip -c /var/lib/cwl/stgedc5ab1b-c488-482a-8696-45842ae2d0b8/GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna.gz | prodigal -d GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/cds.fna -a GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:46:57,791] [INFO] Task succeeded: Prodigal
[2023-06-17 15:46:57,791] [INFO] Task started: HMMsearch
[2023-06-17 15:46:57,792] [INFO] Running command: hmmsearch --tblout GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference/reference_markers.hmm GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:46:58,010] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:46:58,012] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgedc5ab1b-c488-482a-8696-45842ae2d0b8/GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna.gz]
[2023-06-17 15:46:58,027] [INFO] Query marker FASTA was written to GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/markers.fasta
[2023-06-17 15:46:58,028] [INFO] Task started: Blastn
[2023-06-17 15:46:58,028] [INFO] Running command: blastn -query GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference/reference_markers.fasta -out GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:46:59,801] [INFO] Task succeeded: Blastn
[2023-06-17 15:46:59,806] [INFO] Selected 10 target genomes.
[2023-06-17 15:46:59,806] [INFO] Target genome list was writen to GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/target_genomes.txt
[2023-06-17 15:46:59,855] [INFO] Task started: fastANI
[2023-06-17 15:46:59,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgedc5ab1b-c488-482a-8696-45842ae2d0b8/GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna.gz --refList GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/target_genomes.txt --output GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:47:05,945] [INFO] Task succeeded: fastANI
[2023-06-17 15:47:05,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:47:05,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:47:05,948] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 15:47:05,948] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 15:47:05,948] [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
--------------------------------------------------------------------------------
[2023-06-17 15:47:05,950] [INFO] DFAST Taxonomy check result was written to GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/tc_result.tsv
[2023-06-17 15:47:05,951] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:47:05,951] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:47:05,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference/checkm_data
[2023-06-17 15:47:05,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:47:05,972] [INFO] Task started: CheckM
[2023-06-17 15:47:05,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/checkm_input GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/checkm_result
[2023-06-17 15:47:21,906] [INFO] Task succeeded: CheckM
[2023-06-17 15:47:21,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:47:21,929] [INFO] ===== Completeness check finished =====
[2023-06-17 15:47:21,929] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:47:21,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/markers.fasta)
[2023-06-17 15:47:21,930] [INFO] Task started: Blastn
[2023-06-17 15:47:21,931] [INFO] Running command: blastn -query GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefd31c4a-519f-4776-a4aa-be596a94ccaf/dqc_reference/reference_markers_gtdb.fasta -out GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:47:22,808] [INFO] Task succeeded: Blastn
[2023-06-17 15:47:22,818] [INFO] Selected 12 target genomes.
[2023-06-17 15:47:22,819] [INFO] Target genome list was writen to GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:47:22,833] [INFO] Task started: fastANI
[2023-06-17 15:47:22,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgedc5ab1b-c488-482a-8696-45842ae2d0b8/GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna.gz --refList GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/target_genomes_gtdb.txt --output GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:47:26,062] [INFO] Task succeeded: fastANI
[2023-06-17 15:47:26,071] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:47:26,072] [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_002469975.1	s__D2472 sp002469975	99.3464	291	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.56	99.38	0.87	0.81	4	conclusive
GCA_002358345.1	s__D2472 sp002358345	82.2971	269	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.61	97.74	0.92	0.85	27	-
GCA_905181595.1	s__D2472 sp905181595	80.1201	193	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307935.1	s__D2472 sp000307935	77.8546	93	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599315.1	s__D2472 sp902599315	77.584	79	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	97.18	96.37	0.89	0.86	3	-
GCA_902596165.1	s__D2472 sp902596165	77.3064	103	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515775.1	s__D2472 sp902515775	77.2211	67	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	77.2178	75	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902515455.1	s__D2472 sp902515455	77.1257	76	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 15:47:26,074] [INFO] GTDB search result was written to GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/result_gtdb.tsv
[2023-06-17 15:47:26,075] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:47:26,078] [INFO] DFAST_QC result json was written to GCA_905479225.1_0.2_20180522_Bin_MAXBIN_101_sub_1_genomic.fna/dqc_result.json
[2023-06-17 15:47:26,079] [INFO] DFAST_QC completed!
[2023-06-17 15:47:26,079] [INFO] Total running time: 0h0m33s