[2023-06-05 06:46:13,390] [INFO] DFAST_QC pipeline started.
[2023-06-05 06:46:13,393] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 06:46:13,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference
[2023-06-05 06:46:14,721] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 06:46:14,722] [INFO] Task started: Prodigal
[2023-06-05 06:46:14,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg48d77b50-5a54-411d-b332-73933e746da5/GCA_902607435.1_AG-464-G03_genomic.fna.gz | prodigal -d GCA_902607435.1_AG-464-G03_genomic.fna/cds.fna -a GCA_902607435.1_AG-464-G03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 06:46:19,089] [INFO] Task succeeded: Prodigal
[2023-06-05 06:46:19,090] [INFO] Task started: HMMsearch
[2023-06-05 06:46:19,090] [INFO] Running command: hmmsearch --tblout GCA_902607435.1_AG-464-G03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference/reference_markers.hmm GCA_902607435.1_AG-464-G03_genomic.fna/protein.faa > /dev/null
[2023-06-05 06:46:19,361] [INFO] Task succeeded: HMMsearch
[2023-06-05 06:46:19,367] [INFO] Found 6/6 markers.
[2023-06-05 06:46:19,385] [INFO] Query marker FASTA was written to GCA_902607435.1_AG-464-G03_genomic.fna/markers.fasta
[2023-06-05 06:46:19,386] [INFO] Task started: Blastn
[2023-06-05 06:46:19,386] [INFO] Running command: blastn -query GCA_902607435.1_AG-464-G03_genomic.fna/markers.fasta -db /var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference/reference_markers.fasta -out GCA_902607435.1_AG-464-G03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:46:19,975] [INFO] Task succeeded: Blastn
[2023-06-05 06:46:19,979] [INFO] Selected 16 target genomes.
[2023-06-05 06:46:19,979] [INFO] Target genome list was writen to GCA_902607435.1_AG-464-G03_genomic.fna/target_genomes.txt
[2023-06-05 06:46:19,984] [INFO] Task started: fastANI
[2023-06-05 06:46:19,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg48d77b50-5a54-411d-b332-73933e746da5/GCA_902607435.1_AG-464-G03_genomic.fna.gz --refList GCA_902607435.1_AG-464-G03_genomic.fna/target_genomes.txt --output GCA_902607435.1_AG-464-G03_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 06:46:30,656] [INFO] Task succeeded: fastANI
[2023-06-05 06:46:30,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 06:46:30,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 06:46:30,659] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 06:46:30,659] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 06:46:30,659] [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
--------------------------------------------------------------------------------
[2023-06-05 06:46:30,661] [INFO] DFAST Taxonomy check result was written to GCA_902607435.1_AG-464-G03_genomic.fna/tc_result.tsv
[2023-06-05 06:46:30,662] [INFO] ===== Taxonomy check completed =====
[2023-06-05 06:46:30,662] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 06:46:30,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference/checkm_data
[2023-06-05 06:46:30,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 06:46:30,689] [INFO] Task started: CheckM
[2023-06-05 06:46:30,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902607435.1_AG-464-G03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902607435.1_AG-464-G03_genomic.fna/checkm_input GCA_902607435.1_AG-464-G03_genomic.fna/checkm_result
[2023-06-05 06:46:51,169] [INFO] Task succeeded: CheckM
[2023-06-05 06:46:51,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 06:46:51,192] [INFO] ===== Completeness check finished =====
[2023-06-05 06:46:51,192] [INFO] ===== Start GTDB Search =====
[2023-06-05 06:46:51,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902607435.1_AG-464-G03_genomic.fna/markers.fasta)
[2023-06-05 06:46:51,193] [INFO] Task started: Blastn
[2023-06-05 06:46:51,193] [INFO] Running command: blastn -query GCA_902607435.1_AG-464-G03_genomic.fna/markers.fasta -db /var/lib/cwl/stg49081034-fcc9-4ff2-ad04-690dfcf39a5b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902607435.1_AG-464-G03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:46:52,102] [INFO] Task succeeded: Blastn
[2023-06-05 06:46:52,106] [INFO] Selected 16 target genomes.
[2023-06-05 06:46:52,106] [INFO] Target genome list was writen to GCA_902607435.1_AG-464-G03_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 06:46:52,217] [INFO] Task started: fastANI
[2023-06-05 06:46:52,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg48d77b50-5a54-411d-b332-73933e746da5/GCA_902607435.1_AG-464-G03_genomic.fna.gz --refList GCA_902607435.1_AG-464-G03_genomic.fna/target_genomes_gtdb.txt --output GCA_902607435.1_AG-464-G03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 06:46:55,989] [INFO] Task succeeded: fastANI
[2023-06-05 06:46:56,002] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 06:46:56,002] [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_902607435.1	s__CACLJX01 sp902607435	99.9999	483	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACLJX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017639935.1	s__JAGFWP01 sp017639935	78.7397	144	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__JAGFWP01	95.0	99.64	99.12	0.86	0.76	8	-
GCA_002938255.1	s__MarineAlpha5-Bin3 sp002938255	77.6696	88	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	98.64	97.83	0.78	0.73	3	-
GCA_902577425.1	s__MarineAlpha5-Bin3 sp902577425	77.326	127	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_902596065.1	s__MarineAlpha5-Bin3 sp902596065	77.045	84	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597015.1	s__AG-337-I02 sp902597015	77.0213	60	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524385.1	s__AG-337-I02 sp902524385	76.961	77	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560675.1	s__AG-337-I02 sp902554185	76.8317	77	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	98.99	98.59	0.82	0.79	4	-
GCA_002938205.1	s__AG-337-I02 sp002938205	76.8159	112	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	76.7651	105	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
GCA_902586695.1	s__AG-337-I02 sp902586695	76.7297	82	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602515.1	s__AG-337-I02 sp902602515	76.6569	70	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.95	99.95	0.92	0.92	2	-
GCA_902553945.1	s__AG-337-I02 sp902553945	76.3699	71	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282155.1	s__AG-337-I02 sp003282155	76.2538	70	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002937855.1	s__MarineAlpha5-Bin12 sp002937855	75.9867	87	484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin12	95.0	99.77	99.77	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-05 06:46:56,004] [INFO] GTDB search result was written to GCA_902607435.1_AG-464-G03_genomic.fna/result_gtdb.tsv
[2023-06-05 06:46:56,005] [INFO] ===== GTDB Search completed =====
[2023-06-05 06:46:56,008] [INFO] DFAST_QC result json was written to GCA_902607435.1_AG-464-G03_genomic.fna/dqc_result.json
[2023-06-05 06:46:56,008] [INFO] DFAST_QC completed!
[2023-06-05 06:46:56,008] [INFO] Total running time: 0h0m43s