[2023-06-29 07:19:41,737] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:19:41,739] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:19:41,739] [INFO] DQC Reference Directory: /var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference
[2023-06-29 07:19:44,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:19:44,313] [INFO] Task started: Prodigal
[2023-06-29 07:19:44,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg26c6426b-2279-4b90-adfe-4a919fedb5d7/GCA_020624435.1_ASM2062443v1_genomic.fna.gz | prodigal -d GCA_020624435.1_ASM2062443v1_genomic.fna/cds.fna -a GCA_020624435.1_ASM2062443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:19:58,667] [INFO] Task succeeded: Prodigal
[2023-06-29 07:19:58,668] [INFO] Task started: HMMsearch
[2023-06-29 07:19:58,668] [INFO] Running command: hmmsearch --tblout GCA_020624435.1_ASM2062443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference/reference_markers.hmm GCA_020624435.1_ASM2062443v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:19:58,861] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:19:58,863] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg26c6426b-2279-4b90-adfe-4a919fedb5d7/GCA_020624435.1_ASM2062443v1_genomic.fna.gz]
[2023-06-29 07:19:58,900] [INFO] Query marker FASTA was written to GCA_020624435.1_ASM2062443v1_genomic.fna/markers.fasta
[2023-06-29 07:19:58,900] [INFO] Task started: Blastn
[2023-06-29 07:19:58,901] [INFO] Running command: blastn -query GCA_020624435.1_ASM2062443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference/reference_markers.fasta -out GCA_020624435.1_ASM2062443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:19:59,459] [INFO] Task succeeded: Blastn
[2023-06-29 07:19:59,464] [INFO] Selected 21 target genomes.
[2023-06-29 07:19:59,464] [INFO] Target genome list was writen to GCA_020624435.1_ASM2062443v1_genomic.fna/target_genomes.txt
[2023-06-29 07:19:59,466] [INFO] Task started: fastANI
[2023-06-29 07:19:59,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c6426b-2279-4b90-adfe-4a919fedb5d7/GCA_020624435.1_ASM2062443v1_genomic.fna.gz --refList GCA_020624435.1_ASM2062443v1_genomic.fna/target_genomes.txt --output GCA_020624435.1_ASM2062443v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:20:11,352] [INFO] Task succeeded: fastANI
[2023-06-29 07:20:11,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:20:11,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:20:11,356] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:20:11,356] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 07:20:11,357] [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
--------------------------------------------------------------------------------
[2023-06-29 07:20:11,359] [INFO] DFAST Taxonomy check result was written to GCA_020624435.1_ASM2062443v1_genomic.fna/tc_result.tsv
[2023-06-29 07:20:11,360] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:20:11,360] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:20:11,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference/checkm_data
[2023-06-29 07:20:11,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:20:11,403] [INFO] Task started: CheckM
[2023-06-29 07:20:11,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020624435.1_ASM2062443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020624435.1_ASM2062443v1_genomic.fna/checkm_input GCA_020624435.1_ASM2062443v1_genomic.fna/checkm_result
[2023-06-29 07:20:56,069] [INFO] Task succeeded: CheckM
[2023-06-29 07:20:56,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.02%
Contamintation: 33.33%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 07:20:56,097] [INFO] ===== Completeness check finished =====
[2023-06-29 07:20:56,097] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:20:56,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020624435.1_ASM2062443v1_genomic.fna/markers.fasta)
[2023-06-29 07:20:56,098] [INFO] Task started: Blastn
[2023-06-29 07:20:56,099] [INFO] Running command: blastn -query GCA_020624435.1_ASM2062443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc14cac44-1bf3-40bf-8b92-c73e7f54baf6/dqc_reference/reference_markers_gtdb.fasta -out GCA_020624435.1_ASM2062443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:20:56,813] [INFO] Task succeeded: Blastn
[2023-06-29 07:20:56,818] [INFO] Selected 16 target genomes.
[2023-06-29 07:20:56,818] [INFO] Target genome list was writen to GCA_020624435.1_ASM2062443v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:20:56,821] [INFO] Task started: fastANI
[2023-06-29 07:20:56,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg26c6426b-2279-4b90-adfe-4a919fedb5d7/GCA_020624435.1_ASM2062443v1_genomic.fna.gz --refList GCA_020624435.1_ASM2062443v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020624435.1_ASM2062443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:21:04,611] [INFO] Task succeeded: fastANI
[2023-06-29 07:21:04,626] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 07:21:04,627] [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_017449785.1	s__Sodaliphilus sp017449785	79.9135	121	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453505.1	s__Sodaliphilus sp017453505	79.5033	113	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319525.1	s__Sodaliphilus sp900319525	79.4522	110	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.42	97.68	0.92	0.87	5	-
GCA_902793405.1	s__Sodaliphilus sp902793405	79.2879	114	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.00	96.00	0.85	0.85	2	-
GCA_902760865.1	s__Sodaliphilus sp902760865	79.2643	105	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318335.1	s__Sodaliphilus sp900318335	79.2479	112	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.51	96.57	0.89	0.87	11	-
GCA_902776955.1	s__Sodaliphilus sp902776955	78.9067	106	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320245.1	s__Sodaliphilus sp900320245	78.8121	103	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.46	97.77	0.92	0.88	5	-
GCA_900318535.1	s__Sodaliphilus sp900318535	78.6894	105	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.25	96.02	0.89	0.86	17	-
GCA_902792895.1	s__Sodaliphilus sp902792895	78.5818	123	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233915.1	s__Sodaliphilus sp905233915	78.4531	94	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772455.1	s__Sodaliphilus sp902772455	78.4426	108	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787185.1	s__Sodaliphilus sp902787185	78.3901	97	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782465.1	s__Sodaliphilus sp902782465	78.2958	98	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.05	98.05	0.87	0.87	2	-
GCA_900320055.1	s__Sodaliphilus sp900320055	78.2944	101	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.84	98.48	0.90	0.87	16	-
GCA_900317835.1	s__Sodaliphilus sp900317835	77.8155	94	185	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 07:21:04,642] [INFO] GTDB search result was written to GCA_020624435.1_ASM2062443v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:21:04,643] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:21:04,648] [INFO] DFAST_QC result json was written to GCA_020624435.1_ASM2062443v1_genomic.fna/dqc_result.json
[2023-06-29 07:21:04,649] [INFO] DFAST_QC completed!
[2023-06-29 07:21:04,649] [INFO] Total running time: 0h1m23s