[2023-06-17 04:56:48,644] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:56:48,649] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:56:48,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference
[2023-06-17 04:56:49,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:56:50,000] [INFO] Task started: Prodigal
[2023-06-17 04:56:50,000] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7f0c708-bd3c-4b42-82e1-75d9936a6f7d/GCA_003176045.1_ASM317604v1_genomic.fna.gz | prodigal -d GCA_003176045.1_ASM317604v1_genomic.fna/cds.fna -a GCA_003176045.1_ASM317604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:57:36,192] [INFO] Task succeeded: Prodigal
[2023-06-17 04:57:36,192] [INFO] Task started: HMMsearch
[2023-06-17 04:57:36,192] [INFO] Running command: hmmsearch --tblout GCA_003176045.1_ASM317604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference/reference_markers.hmm GCA_003176045.1_ASM317604v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:57:36,527] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:57:36,528] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc7f0c708-bd3c-4b42-82e1-75d9936a6f7d/GCA_003176045.1_ASM317604v1_genomic.fna.gz]
[2023-06-17 04:57:36,583] [INFO] Query marker FASTA was written to GCA_003176045.1_ASM317604v1_genomic.fna/markers.fasta
[2023-06-17 04:57:36,584] [INFO] Task started: Blastn
[2023-06-17 04:57:36,584] [INFO] Running command: blastn -query GCA_003176045.1_ASM317604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference/reference_markers.fasta -out GCA_003176045.1_ASM317604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:37,219] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:37,226] [INFO] Selected 12 target genomes.
[2023-06-17 04:57:37,227] [INFO] Target genome list was writen to GCA_003176045.1_ASM317604v1_genomic.fna/target_genomes.txt
[2023-06-17 04:57:37,236] [INFO] Task started: fastANI
[2023-06-17 04:57:37,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f0c708-bd3c-4b42-82e1-75d9936a6f7d/GCA_003176045.1_ASM317604v1_genomic.fna.gz --refList GCA_003176045.1_ASM317604v1_genomic.fna/target_genomes.txt --output GCA_003176045.1_ASM317604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:57:43,470] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:43,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:57:43,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:57:43,473] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:57:43,473] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 04:57:43,473] [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
--------------------------------------------------------------------------------
[2023-06-17 04:57:43,476] [INFO] DFAST Taxonomy check result was written to GCA_003176045.1_ASM317604v1_genomic.fna/tc_result.tsv
[2023-06-17 04:57:43,476] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:57:43,476] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:57:43,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference/checkm_data
[2023-06-17 04:57:43,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:57:43,555] [INFO] Task started: CheckM
[2023-06-17 04:57:43,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003176045.1_ASM317604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003176045.1_ASM317604v1_genomic.fna/checkm_input GCA_003176045.1_ASM317604v1_genomic.fna/checkm_result
[2023-06-17 04:59:43,271] [INFO] Task succeeded: CheckM
[2023-06-17 04:59:43,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:59:43,298] [INFO] ===== Completeness check finished =====
[2023-06-17 04:59:43,298] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:59:43,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003176045.1_ASM317604v1_genomic.fna/markers.fasta)
[2023-06-17 04:59:43,299] [INFO] Task started: Blastn
[2023-06-17 04:59:43,299] [INFO] Running command: blastn -query GCA_003176045.1_ASM317604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ec8f9a1-ebc3-403e-aa5f-2e8eda303710/dqc_reference/reference_markers_gtdb.fasta -out GCA_003176045.1_ASM317604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:59:44,341] [INFO] Task succeeded: Blastn
[2023-06-17 04:59:44,347] [INFO] Selected 21 target genomes.
[2023-06-17 04:59:44,347] [INFO] Target genome list was writen to GCA_003176045.1_ASM317604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:59:44,355] [INFO] Task started: fastANI
[2023-06-17 04:59:44,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f0c708-bd3c-4b42-82e1-75d9936a6f7d/GCA_003176045.1_ASM317604v1_genomic.fna.gz --refList GCA_003176045.1_ASM317604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003176045.1_ASM317604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:00:06,293] [INFO] Task succeeded: fastANI
[2023-06-17 05:00:06,316] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:00:06,316] [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_003176045.1	s__PSRM01 sp003176045	100.0	2375	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PSRM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011525685.1	s__WYBW01 sp011525685	75.6346	116	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871535.1	s__VHCZ01 sp016871535	75.527	78	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIBE01;g__VHCZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152225.1	s__PALSA-1440 sp003152225	75.514	136	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385705.1	s__UBA3939 sp002385705	75.5039	71	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_903912925.1	s__PALSA-1440 sp903912925	75.4641	143	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367605.1	s__DSYF01 sp011367605	75.4301	70	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__DSYF01;g__DSYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695195.1	s__SCTL01 sp009695195	75.3099	77	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__SCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003219345.1	s__AV2 sp003219345	75.2801	72	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AV2;g__AV2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921455.1	s__UBA11358 sp903921455	75.2598	63	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298785.1	s__UBA693 sp002298785	75.2375	72	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__UBA693	95.0	99.38	99.38	0.89	0.89	2	-
GCA_003134375.1	s__UBA7542 sp003134375	75.1545	73	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA7542	95.0	99.88	99.76	0.95	0.91	18	-
GCA_003161635.1	s__UBA7542 sp003161635	75.1459	96	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA7542	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200005.1	s__PALSA-1396 sp016200005	75.1337	105	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__PALSA-1396;g__PALSA-1396	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140095.1	s__Palsa-1400 sp003140095	75.1177	79	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Palsa-1400;g__Palsa-1400	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870815.1	s__UBA11358 sp903870815	75.0865	55	2390	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.83	99.83	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-17 05:00:06,318] [INFO] GTDB search result was written to GCA_003176045.1_ASM317604v1_genomic.fna/result_gtdb.tsv
[2023-06-17 05:00:06,319] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:00:06,322] [INFO] DFAST_QC result json was written to GCA_003176045.1_ASM317604v1_genomic.fna/dqc_result.json
[2023-06-17 05:00:06,323] [INFO] DFAST_QC completed!
[2023-06-17 05:00:06,323] [INFO] Total running time: 0h3m18s