[2023-06-05 05:15:24,713] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:24,716] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:24,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference
[2023-06-05 05:15:26,470] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:26,471] [INFO] Task started: Prodigal
[2023-06-05 05:15:26,472] [INFO] Running command: gunzip -c /var/lib/cwl/stgef805e17-0cc0-4cb3-b09c-4933e8b554a2/GCA_004555145.1_ASM455514v1_genomic.fna.gz | prodigal -d GCA_004555145.1_ASM455514v1_genomic.fna/cds.fna -a GCA_004555145.1_ASM455514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:35,616] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:35,617] [INFO] Task started: HMMsearch
[2023-06-05 05:15:35,617] [INFO] Running command: hmmsearch --tblout GCA_004555145.1_ASM455514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference/reference_markers.hmm GCA_004555145.1_ASM455514v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:35,864] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:35,865] [INFO] Found 6/6 markers.
[2023-06-05 05:15:35,889] [INFO] Query marker FASTA was written to GCA_004555145.1_ASM455514v1_genomic.fna/markers.fasta
[2023-06-05 05:15:35,889] [INFO] Task started: Blastn
[2023-06-05 05:15:35,889] [INFO] Running command: blastn -query GCA_004555145.1_ASM455514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference/reference_markers.fasta -out GCA_004555145.1_ASM455514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:15:36,450] [INFO] Task succeeded: Blastn
[2023-06-05 05:15:36,454] [INFO] Selected 35 target genomes.
[2023-06-05 05:15:36,454] [INFO] Target genome list was writen to GCA_004555145.1_ASM455514v1_genomic.fna/target_genomes.txt
[2023-06-05 05:15:36,493] [INFO] Task started: fastANI
[2023-06-05 05:15:36,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgef805e17-0cc0-4cb3-b09c-4933e8b554a2/GCA_004555145.1_ASM455514v1_genomic.fna.gz --refList GCA_004555145.1_ASM455514v1_genomic.fna/target_genomes.txt --output GCA_004555145.1_ASM455514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:15:55,413] [INFO] Task succeeded: fastANI
[2023-06-05 05:15:55,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:15:55,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:15:55,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:15:55,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:15:55,417] [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 05:15:55,418] [INFO] DFAST Taxonomy check result was written to GCA_004555145.1_ASM455514v1_genomic.fna/tc_result.tsv
[2023-06-05 05:15:55,419] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:15:55,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:15:55,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference/checkm_data
[2023-06-05 05:15:55,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:15:55,445] [INFO] Task started: CheckM
[2023-06-05 05:15:55,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004555145.1_ASM455514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004555145.1_ASM455514v1_genomic.fna/checkm_input GCA_004555145.1_ASM455514v1_genomic.fna/checkm_result
[2023-06-05 05:16:26,356] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:26,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 8.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:26,380] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:26,380] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:26,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004555145.1_ASM455514v1_genomic.fna/markers.fasta)
[2023-06-05 05:16:26,381] [INFO] Task started: Blastn
[2023-06-05 05:16:26,381] [INFO] Running command: blastn -query GCA_004555145.1_ASM455514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg988f3422-92f3-4b3c-b7a8-59089e120fe6/dqc_reference/reference_markers_gtdb.fasta -out GCA_004555145.1_ASM455514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:27,225] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:27,231] [INFO] Selected 21 target genomes.
[2023-06-05 05:16:27,231] [INFO] Target genome list was writen to GCA_004555145.1_ASM455514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:27,236] [INFO] Task started: fastANI
[2023-06-05 05:16:27,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgef805e17-0cc0-4cb3-b09c-4933e8b554a2/GCA_004555145.1_ASM455514v1_genomic.fna.gz --refList GCA_004555145.1_ASM455514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004555145.1_ASM455514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:16:34,157] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:34,178] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:16:34,178] [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_004555145.1	s__Cryptobacteroides sp004555145	100.0	464	469	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_900769905.1	s__Cryptobacteroides sp900769905	87.505	329	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
GCA_016295245.1	s__Cryptobacteroides sp016295245	78.4726	107	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.61	98.61	0.79	0.79	2	-
GCA_900541925.1	s__Cryptobacteroides sp900541925	78.1063	140	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.89	97.86	0.90	0.88	3	-
GCA_002439095.1	s__Cryptobacteroides sp002439095	77.9397	126	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.02	98.66	0.95	0.93	5	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	77.8055	115	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	77.7967	100	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432655.1	s__Cryptobacteroides sp000432655	77.7444	133	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.19	97.59	0.89	0.80	6	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	77.7402	116	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	77.7334	121	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	77.6585	92	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789245.1	s__Cryptobacteroides sp902789245	77.6321	113	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_002438805.1	s__Cryptobacteroides sp002438805	77.6213	133	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.44	99.33	0.95	0.94	4	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	77.5651	65	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	77.4915	114	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
GCA_017561865.1	s__Cryptobacteroides sp017561865	77.3289	70	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234475.1	s__Cryptobacteroides sp905234475	77.3097	105	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	77.1494	54	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	77.0067	51	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	76.8454	57	469	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
--------------------------------------------------------------------------------
[2023-06-05 05:16:34,180] [INFO] GTDB search result was written to GCA_004555145.1_ASM455514v1_genomic.fna/result_gtdb.tsv
[2023-06-05 05:16:34,181] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:16:34,186] [INFO] DFAST_QC result json was written to GCA_004555145.1_ASM455514v1_genomic.fna/dqc_result.json
[2023-06-05 05:16:34,187] [INFO] DFAST_QC completed!
[2023-06-05 05:16:34,187] [INFO] Total running time: 0h1m9s