[2023-06-30 21:40:32,747] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:40:32,748] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:40:32,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference
[2023-06-30 21:40:34,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:40:34,914] [INFO] Task started: Prodigal
[2023-06-30 21:40:34,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a9c3285-056c-40da-91bd-1af445be2cf7/GCA_016281295.1_ASM1628129v1_genomic.fna.gz | prodigal -d GCA_016281295.1_ASM1628129v1_genomic.fna/cds.fna -a GCA_016281295.1_ASM1628129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:40:54,870] [INFO] Task succeeded: Prodigal
[2023-06-30 21:40:54,870] [INFO] Task started: HMMsearch
[2023-06-30 21:40:54,870] [INFO] Running command: hmmsearch --tblout GCA_016281295.1_ASM1628129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference/reference_markers.hmm GCA_016281295.1_ASM1628129v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:40:55,169] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:40:55,171] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a9c3285-056c-40da-91bd-1af445be2cf7/GCA_016281295.1_ASM1628129v1_genomic.fna.gz]
[2023-06-30 21:40:55,204] [INFO] Query marker FASTA was written to GCA_016281295.1_ASM1628129v1_genomic.fna/markers.fasta
[2023-06-30 21:40:55,205] [INFO] Task started: Blastn
[2023-06-30 21:40:55,205] [INFO] Running command: blastn -query GCA_016281295.1_ASM1628129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference/reference_markers.fasta -out GCA_016281295.1_ASM1628129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:40:55,769] [INFO] Task succeeded: Blastn
[2023-06-30 21:40:55,772] [INFO] Selected 22 target genomes.
[2023-06-30 21:40:55,773] [INFO] Target genome list was writen to GCA_016281295.1_ASM1628129v1_genomic.fna/target_genomes.txt
[2023-06-30 21:40:55,780] [INFO] Task started: fastANI
[2023-06-30 21:40:55,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a9c3285-056c-40da-91bd-1af445be2cf7/GCA_016281295.1_ASM1628129v1_genomic.fna.gz --refList GCA_016281295.1_ASM1628129v1_genomic.fna/target_genomes.txt --output GCA_016281295.1_ASM1628129v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:41:12,453] [INFO] Task succeeded: fastANI
[2023-06-30 21:41:12,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:41:12,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:41:12,456] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:41:12,456] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:41:12,456] [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
--------------------------------------------------------------------------------
[2023-06-30 21:41:12,458] [INFO] DFAST Taxonomy check result was written to GCA_016281295.1_ASM1628129v1_genomic.fna/tc_result.tsv
[2023-06-30 21:41:12,458] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:41:12,459] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:41:12,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference/checkm_data
[2023-06-30 21:41:12,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:41:12,503] [INFO] Task started: CheckM
[2023-06-30 21:41:12,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016281295.1_ASM1628129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016281295.1_ASM1628129v1_genomic.fna/checkm_input GCA_016281295.1_ASM1628129v1_genomic.fna/checkm_result
[2023-06-30 21:42:11,317] [INFO] Task succeeded: CheckM
[2023-06-30 21:42:11,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.45%
Contamintation: 27.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 21:42:11,347] [INFO] ===== Completeness check finished =====
[2023-06-30 21:42:11,348] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:42:11,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016281295.1_ASM1628129v1_genomic.fna/markers.fasta)
[2023-06-30 21:42:11,349] [INFO] Task started: Blastn
[2023-06-30 21:42:11,349] [INFO] Running command: blastn -query GCA_016281295.1_ASM1628129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f8eb8b-736e-4f5b-a56d-515172b22c5a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016281295.1_ASM1628129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:42:12,108] [INFO] Task succeeded: Blastn
[2023-06-30 21:42:12,114] [INFO] Selected 20 target genomes.
[2023-06-30 21:42:12,114] [INFO] Target genome list was writen to GCA_016281295.1_ASM1628129v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:42:12,163] [INFO] Task started: fastANI
[2023-06-30 21:42:12,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a9c3285-056c-40da-91bd-1af445be2cf7/GCA_016281295.1_ASM1628129v1_genomic.fna.gz --refList GCA_016281295.1_ASM1628129v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016281295.1_ASM1628129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:42:22,451] [INFO] Task succeeded: fastANI
[2023-06-30 21:42:22,476] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:42:22,477] [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_016281295.1	s__Limimorpha sp016281295	100.0	984	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902783365.1	s__Limimorpha sp902783365	80.2681	327	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291135.1	s__Limimorpha sp016291135	80.1678	340	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017530365.1	s__Limimorpha sp017530365	79.9127	329	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800965.1	s__Limimorpha sp902800965	79.8597	324	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.93	97.90	0.89	0.89	3	-
GCA_016284305.1	s__Limimorpha sp016284305	79.7356	323	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.90	97.90	0.83	0.83	2	-
GCA_017965765.1	s__Limimorpha sp017965765	79.5924	263	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.54	95.54	0.71	0.71	2	-
GCA_017645245.1	s__Limimorpha sp017645245	79.5169	268	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017537965.1	s__Limimorpha sp017537965	79.4947	293	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017531225.1	s__Limimorpha sp017531225	79.4753	267	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.56	96.56	0.77	0.77	2	-
GCA_902786745.1	s__Limimorpha sp902786745	78.841	238	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.85	95.75	0.88	0.85	4	-
GCA_902774365.1	s__Limimorpha sp902774365	78.759	226	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789915.1	s__Limimorpha sp902789915	78.537	175	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.09	95.09	0.73	0.73	2	-
GCA_016290215.1	s__Limimorpha sp016290215	78.3728	234	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234645.1	s__Limimorpha sp905234645	77.9176	208	992	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:42:22,479] [INFO] GTDB search result was written to GCA_016281295.1_ASM1628129v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:42:22,479] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:42:22,483] [INFO] DFAST_QC result json was written to GCA_016281295.1_ASM1628129v1_genomic.fna/dqc_result.json
[2023-06-30 21:42:22,483] [INFO] DFAST_QC completed!
[2023-06-30 21:42:22,483] [INFO] Total running time: 0h1m50s