[2023-06-05 10:33:52,683] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:52,685] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:52,685] [INFO] DQC Reference Directory: /var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference
[2023-06-05 10:33:53,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:53,989] [INFO] Task started: Prodigal
[2023-06-05 10:33:53,989] [INFO] Running command: gunzip -c /var/lib/cwl/stgc39e231f-ef11-45df-9c8a-ca8c4c52ca72/GCA_001769045.1_ASM176904v1_genomic.fna.gz | prodigal -d GCA_001769045.1_ASM176904v1_genomic.fna/cds.fna -a GCA_001769045.1_ASM176904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:34:06,276] [INFO] Task succeeded: Prodigal
[2023-06-05 10:34:06,276] [INFO] Task started: HMMsearch
[2023-06-05 10:34:06,276] [INFO] Running command: hmmsearch --tblout GCA_001769045.1_ASM176904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference/reference_markers.hmm GCA_001769045.1_ASM176904v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:34:06,557] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:34:06,558] [INFO] Found 6/6 markers.
[2023-06-05 10:34:06,592] [INFO] Query marker FASTA was written to GCA_001769045.1_ASM176904v1_genomic.fna/markers.fasta
[2023-06-05 10:34:06,593] [INFO] Task started: Blastn
[2023-06-05 10:34:06,593] [INFO] Running command: blastn -query GCA_001769045.1_ASM176904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference/reference_markers.fasta -out GCA_001769045.1_ASM176904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:07,205] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:07,210] [INFO] Selected 25 target genomes.
[2023-06-05 10:34:07,211] [INFO] Target genome list was writen to GCA_001769045.1_ASM176904v1_genomic.fna/target_genomes.txt
[2023-06-05 10:34:07,215] [INFO] Task started: fastANI
[2023-06-05 10:34:07,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39e231f-ef11-45df-9c8a-ca8c4c52ca72/GCA_001769045.1_ASM176904v1_genomic.fna.gz --refList GCA_001769045.1_ASM176904v1_genomic.fna/target_genomes.txt --output GCA_001769045.1_ASM176904v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:34:23,198] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:23,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:34:23,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:34:23,202] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:34:23,202] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:34:23,202] [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 10:34:23,204] [INFO] DFAST Taxonomy check result was written to GCA_001769045.1_ASM176904v1_genomic.fna/tc_result.tsv
[2023-06-05 10:34:23,205] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:34:23,206] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:34:23,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference/checkm_data
[2023-06-05 10:34:23,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:34:23,252] [INFO] Task started: CheckM
[2023-06-05 10:34:23,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001769045.1_ASM176904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001769045.1_ASM176904v1_genomic.fna/checkm_input GCA_001769045.1_ASM176904v1_genomic.fna/checkm_result
[2023-06-05 10:35:02,018] [INFO] Task succeeded: CheckM
[2023-06-05 10:35:02,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:35:02,044] [INFO] ===== Completeness check finished =====
[2023-06-05 10:35:02,044] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:35:02,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001769045.1_ASM176904v1_genomic.fna/markers.fasta)
[2023-06-05 10:35:02,045] [INFO] Task started: Blastn
[2023-06-05 10:35:02,045] [INFO] Running command: blastn -query GCA_001769045.1_ASM176904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd86ae5e1-f55f-47d2-8491-8e58c4d13459/dqc_reference/reference_markers_gtdb.fasta -out GCA_001769045.1_ASM176904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:35:02,838] [INFO] Task succeeded: Blastn
[2023-06-05 10:35:02,846] [INFO] Selected 19 target genomes.
[2023-06-05 10:35:02,846] [INFO] Target genome list was writen to GCA_001769045.1_ASM176904v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:35:02,855] [INFO] Task started: fastANI
[2023-06-05 10:35:02,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39e231f-ef11-45df-9c8a-ca8c4c52ca72/GCA_001769045.1_ASM176904v1_genomic.fna.gz --refList GCA_001769045.1_ASM176904v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001769045.1_ASM176904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:35:15,229] [INFO] Task succeeded: fastANI
[2023-06-05 10:35:15,241] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:35:15,242] [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_001768235.1	s__UBA12077 sp001768235	99.9906	1190	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	99.99	99.99	0.99	0.99	5	conclusive
GCA_001769005.1	s__UBA12077 sp001769005	80.5473	578	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768565.1	s__UBA12077 sp001768565	78.3931	410	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003446015.1	s__UBA12077 sp003446015	77.2363	233	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019038645.1	s__UBA12077 sp019038645	76.6371	173	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342685.1	s__UBA12077 sp016342685	76.5221	183	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869305.1	s__UBA12077 sp002869305	76.343	109	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769505.1	s__GWF2-33-38 sp001769505	75.7718	59	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-33-38;g__GWF2-33-38	95.0	99.92	99.84	0.98	0.98	4	-
GCA_903837285.1	s__GWA2-32-17 sp903837285	75.1878	60	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	99.88	99.88	0.97	0.97	2	-
GCA_001769035.1	s__GWA2-32-17 sp001769035	75.1566	60	1202	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:35:15,244] [INFO] GTDB search result was written to GCA_001769045.1_ASM176904v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:35:15,245] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:35:15,247] [INFO] DFAST_QC result json was written to GCA_001769045.1_ASM176904v1_genomic.fna/dqc_result.json
[2023-06-05 10:35:15,248] [INFO] DFAST_QC completed!
[2023-06-05 10:35:15,248] [INFO] Total running time: 0h1m23s