[2023-06-18 22:56:45,531] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:56:45,534] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:56:45,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference
[2023-06-18 22:56:46,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:56:46,895] [INFO] Task started: Prodigal
[2023-06-18 22:56:46,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg5289f516-5f9e-42b5-b119-190acedbed2f/GCA_018065985.1_ASM1806598v1_genomic.fna.gz | prodigal -d GCA_018065985.1_ASM1806598v1_genomic.fna/cds.fna -a GCA_018065985.1_ASM1806598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:57:00,117] [INFO] Task succeeded: Prodigal
[2023-06-18 22:57:00,117] [INFO] Task started: HMMsearch
[2023-06-18 22:57:00,117] [INFO] Running command: hmmsearch --tblout GCA_018065985.1_ASM1806598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference/reference_markers.hmm GCA_018065985.1_ASM1806598v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:57:00,379] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:57:00,381] [INFO] Found 6/6 markers.
[2023-06-18 22:57:00,406] [INFO] Query marker FASTA was written to GCA_018065985.1_ASM1806598v1_genomic.fna/markers.fasta
[2023-06-18 22:57:00,407] [INFO] Task started: Blastn
[2023-06-18 22:57:00,407] [INFO] Running command: blastn -query GCA_018065985.1_ASM1806598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference/reference_markers.fasta -out GCA_018065985.1_ASM1806598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:01,011] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:01,015] [INFO] Selected 34 target genomes.
[2023-06-18 22:57:01,015] [INFO] Target genome list was writen to GCA_018065985.1_ASM1806598v1_genomic.fna/target_genomes.txt
[2023-06-18 22:57:01,018] [INFO] Task started: fastANI
[2023-06-18 22:57:01,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg5289f516-5f9e-42b5-b119-190acedbed2f/GCA_018065985.1_ASM1806598v1_genomic.fna.gz --refList GCA_018065985.1_ASM1806598v1_genomic.fna/target_genomes.txt --output GCA_018065985.1_ASM1806598v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:20,302] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:20,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:20,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:20,304] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:20,304] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:57:20,305] [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
--------------------------------------------------------------------------------
[2023-06-18 22:57:20,307] [INFO] DFAST Taxonomy check result was written to GCA_018065985.1_ASM1806598v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:20,307] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:20,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:20,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference/checkm_data
[2023-06-18 22:57:20,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:20,337] [INFO] Task started: CheckM
[2023-06-18 22:57:20,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018065985.1_ASM1806598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018065985.1_ASM1806598v1_genomic.fna/checkm_input GCA_018065985.1_ASM1806598v1_genomic.fna/checkm_result
[2023-06-18 22:58:02,050] [INFO] Task succeeded: CheckM
[2023-06-18 22:58:02,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.55%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 22:58:02,071] [INFO] ===== Completeness check finished =====
[2023-06-18 22:58:02,071] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:58:02,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018065985.1_ASM1806598v1_genomic.fna/markers.fasta)
[2023-06-18 22:58:02,072] [INFO] Task started: Blastn
[2023-06-18 22:58:02,072] [INFO] Running command: blastn -query GCA_018065985.1_ASM1806598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a388ebf-7fe0-4e17-a772-a6487530af26/dqc_reference/reference_markers_gtdb.fasta -out GCA_018065985.1_ASM1806598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:58:02,942] [INFO] Task succeeded: Blastn
[2023-06-18 22:58:02,947] [INFO] Selected 25 target genomes.
[2023-06-18 22:58:02,947] [INFO] Target genome list was writen to GCA_018065985.1_ASM1806598v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:58:02,956] [INFO] Task started: fastANI
[2023-06-18 22:58:02,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg5289f516-5f9e-42b5-b119-190acedbed2f/GCA_018065985.1_ASM1806598v1_genomic.fna.gz --refList GCA_018065985.1_ASM1806598v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018065985.1_ASM1806598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:58:11,782] [INFO] Task succeeded: fastANI
[2023-06-18 22:58:11,803] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:58:11,804] [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_018065985.1	s__Cryptobacteroides sp018065985	100.0	709	714	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_018064625.1	s__Cryptobacteroides sp018064625	78.7494	95	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787295.1	s__Cryptobacteroides sp902787295	78.4892	142	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.75	97.75	0.73	0.73	2	-
GCA_900771005.1	s__Cryptobacteroides sp900771005	78.3414	82	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782225.1	s__Cryptobacteroides sp902782225	78.0789	129	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	97.13	0.87	0.83	3	-
GCA_016295245.1	s__Cryptobacteroides sp016295245	77.9412	96	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.61	98.61	0.79	0.79	2	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	77.8372	135	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	77.8278	143	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_905235775.1	s__Cryptobacteroides sp905235775	77.7227	103	714	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	77.6874	145	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	77.6061	105	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_017455065.1	s__Cryptobacteroides sp017455065	77.5834	129	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002315815.1	s__Cryptobacteroides sp002315815	77.4175	62	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066125.1	s__Cryptobacteroides sp018066125	77.3944	127	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167925.1	s__Cryptobacteroides sp900167925	77.393	74	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.91	97.12	0.93	0.91	9	-
GCA_902792815.1	s__Cryptobacteroides sp902792815	77.3913	104	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.52	96.82	0.86	0.75	13	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	77.3798	110	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554335.1	s__Cryptobacteroides sp017554335	77.3589	121	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651225.1	s__Cryptobacteroides sp017651225	77.2104	120	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017962925.1	s__Cryptobacteroides sp017962925	76.7759	78	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290725.1	s__Cryptobacteroides sp016290725	76.5588	56	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.90	98.90	0.76	0.76	2	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	76.5573	62	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320185.1	s__Cryptobacteroides sp900320185	76.5534	73	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.37	0.88	0.82	11	-
GCA_017444905.1	s__Cryptobacteroides sp017444905	76.3045	61	714	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:58:11,805] [INFO] GTDB search result was written to GCA_018065985.1_ASM1806598v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:58:11,806] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:58:11,809] [INFO] DFAST_QC result json was written to GCA_018065985.1_ASM1806598v1_genomic.fna/dqc_result.json
[2023-06-18 22:58:11,809] [INFO] DFAST_QC completed!
[2023-06-18 22:58:11,809] [INFO] Total running time: 0h1m26s