[2023-06-28 17:03:06,349] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:03:06,352] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:03:06,352] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference
[2023-06-28 17:03:07,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:03:07,638] [INFO] Task started: Prodigal
[2023-06-28 17:03:07,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f6392ce-a4a9-45d0-abab-b89ffe4353be/GCA_017626355.1_ASM1762635v1_genomic.fna.gz | prodigal -d GCA_017626355.1_ASM1762635v1_genomic.fna/cds.fna -a GCA_017626355.1_ASM1762635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:03:16,417] [INFO] Task succeeded: Prodigal
[2023-06-28 17:03:16,417] [INFO] Task started: HMMsearch
[2023-06-28 17:03:16,418] [INFO] Running command: hmmsearch --tblout GCA_017626355.1_ASM1762635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference/reference_markers.hmm GCA_017626355.1_ASM1762635v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:03:16,692] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:03:16,695] [INFO] Found 6/6 markers.
[2023-06-28 17:03:16,714] [INFO] Query marker FASTA was written to GCA_017626355.1_ASM1762635v1_genomic.fna/markers.fasta
[2023-06-28 17:03:16,714] [INFO] Task started: Blastn
[2023-06-28 17:03:16,715] [INFO] Running command: blastn -query GCA_017626355.1_ASM1762635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference/reference_markers.fasta -out GCA_017626355.1_ASM1762635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:03:17,275] [INFO] Task succeeded: Blastn
[2023-06-28 17:03:17,279] [INFO] Selected 26 target genomes.
[2023-06-28 17:03:17,279] [INFO] Target genome list was writen to GCA_017626355.1_ASM1762635v1_genomic.fna/target_genomes.txt
[2023-06-28 17:03:17,280] [INFO] Task started: fastANI
[2023-06-28 17:03:17,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f6392ce-a4a9-45d0-abab-b89ffe4353be/GCA_017626355.1_ASM1762635v1_genomic.fna.gz --refList GCA_017626355.1_ASM1762635v1_genomic.fna/target_genomes.txt --output GCA_017626355.1_ASM1762635v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:03:33,234] [INFO] Task succeeded: fastANI
[2023-06-28 17:03:33,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:03:33,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:03:33,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:03:33,237] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:03:33,238] [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
--------------------------------------------------------------------------------
[2023-06-28 17:03:33,240] [INFO] DFAST Taxonomy check result was written to GCA_017626355.1_ASM1762635v1_genomic.fna/tc_result.tsv
[2023-06-28 17:03:33,241] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:03:33,241] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:03:33,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference/checkm_data
[2023-06-28 17:03:33,246] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:03:33,269] [INFO] Task started: CheckM
[2023-06-28 17:03:33,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017626355.1_ASM1762635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017626355.1_ASM1762635v1_genomic.fna/checkm_input GCA_017626355.1_ASM1762635v1_genomic.fna/checkm_result
[2023-06-28 17:04:04,476] [INFO] Task succeeded: CheckM
[2023-06-28 17:04:04,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.86%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:04:04,499] [INFO] ===== Completeness check finished =====
[2023-06-28 17:04:04,499] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:04:04,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017626355.1_ASM1762635v1_genomic.fna/markers.fasta)
[2023-06-28 17:04:04,500] [INFO] Task started: Blastn
[2023-06-28 17:04:04,500] [INFO] Running command: blastn -query GCA_017626355.1_ASM1762635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbc12b51-935c-4a64-b66c-d27e7a1f4459/dqc_reference/reference_markers_gtdb.fasta -out GCA_017626355.1_ASM1762635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:04:05,273] [INFO] Task succeeded: Blastn
[2023-06-28 17:04:05,277] [INFO] Selected 22 target genomes.
[2023-06-28 17:04:05,277] [INFO] Target genome list was writen to GCA_017626355.1_ASM1762635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:04:05,280] [INFO] Task started: fastANI
[2023-06-28 17:04:05,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f6392ce-a4a9-45d0-abab-b89ffe4353be/GCA_017626355.1_ASM1762635v1_genomic.fna.gz --refList GCA_017626355.1_ASM1762635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017626355.1_ASM1762635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:04:13,615] [INFO] Task succeeded: fastANI
[2023-06-28 17:04:13,637] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:04:13,637] [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_017626355.1	s__Cryptobacteroides sp017626355	100.0	553	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017465225.1	s__Cryptobacteroides sp017465225	80.9681	225	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.02	96.60	0.67	0.61	4	-
GCA_017437125.1	s__Cryptobacteroides sp017437125	80.6875	224	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937885.1	s__Cryptobacteroides sp017937885	80.2078	178	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561265.1	s__Cryptobacteroides sp017561265	80.1124	166	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060395.1	s__Cryptobacteroides sp015060395	79.9791	226	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.90	97.87	0.88	0.85	4	-
GCA_015060385.1	s__Cryptobacteroides sp015060385	79.9442	192	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060405.1	s__Cryptobacteroides sp015060405	79.7846	216	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549505.1	s__Cryptobacteroides sp017549505	79.6917	183	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461285.1	s__Cryptobacteroides sp017461285	79.6874	216	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415715.1	s__Cryptobacteroides sp017415715	79.644	210	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060325.1	s__Cryptobacteroides sp015060325	79.5668	173	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399905.1	s__Cryptobacteroides sp017399905	79.5515	218	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.58	97.58	0.79	0.79	2	-
GCA_017398335.1	s__Cryptobacteroides sp017398335	79.441	151	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017502125.1	s__Cryptobacteroides sp017502125	79.367	196	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556765.1	s__Cryptobacteroides sp017556765	79.3167	173	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017630215.1	s__Cryptobacteroides sp017630215	79.2625	133	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017506825.1	s__Cryptobacteroides sp017506825	79.2617	108	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472115.1	s__Cryptobacteroides sp017472115	79.1281	153	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017560825.1	s__Cryptobacteroides sp017560825	78.8924	175	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.79	95.07	0.79	0.69	4	-
GCA_017625725.1	s__Cryptobacteroides sp017625725	78.4441	150	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585445.1	s__Cryptobacteroides sp910585445	78.1038	143	553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.74	96.72	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-28 17:04:13,639] [INFO] GTDB search result was written to GCA_017626355.1_ASM1762635v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:04:13,640] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:04:13,643] [INFO] DFAST_QC result json was written to GCA_017626355.1_ASM1762635v1_genomic.fna/dqc_result.json
[2023-06-28 17:04:13,644] [INFO] DFAST_QC completed!
[2023-06-28 17:04:13,644] [INFO] Total running time: 0h1m7s