[2023-06-30 09:37:05,079] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:37:05,085] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:37:05,085] [INFO] DQC Reference Directory: /var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference
[2023-06-30 09:37:06,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:37:06,571] [INFO] Task started: Prodigal
[2023-06-30 09:37:06,572] [INFO] Running command: gunzip -c /var/lib/cwl/stga7e65687-b083-46f7-8e3d-70afd7085818/GCA_016708015.1_ASM1670801v1_genomic.fna.gz | prodigal -d GCA_016708015.1_ASM1670801v1_genomic.fna/cds.fna -a GCA_016708015.1_ASM1670801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:37:22,414] [INFO] Task succeeded: Prodigal
[2023-06-30 09:37:22,414] [INFO] Task started: HMMsearch
[2023-06-30 09:37:22,414] [INFO] Running command: hmmsearch --tblout GCA_016708015.1_ASM1670801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference/reference_markers.hmm GCA_016708015.1_ASM1670801v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:37:22,720] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:37:22,721] [INFO] Found 6/6 markers.
[2023-06-30 09:37:22,765] [INFO] Query marker FASTA was written to GCA_016708015.1_ASM1670801v1_genomic.fna/markers.fasta
[2023-06-30 09:37:22,766] [INFO] Task started: Blastn
[2023-06-30 09:37:22,766] [INFO] Running command: blastn -query GCA_016708015.1_ASM1670801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference/reference_markers.fasta -out GCA_016708015.1_ASM1670801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:37:23,376] [INFO] Task succeeded: Blastn
[2023-06-30 09:37:23,380] [INFO] Selected 31 target genomes.
[2023-06-30 09:37:23,380] [INFO] Target genome list was writen to GCA_016708015.1_ASM1670801v1_genomic.fna/target_genomes.txt
[2023-06-30 09:37:23,383] [INFO] Task started: fastANI
[2023-06-30 09:37:23,384] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e65687-b083-46f7-8e3d-70afd7085818/GCA_016708015.1_ASM1670801v1_genomic.fna.gz --refList GCA_016708015.1_ASM1670801v1_genomic.fna/target_genomes.txt --output GCA_016708015.1_ASM1670801v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:37:46,048] [INFO] Task succeeded: fastANI
[2023-06-30 09:37:46,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:37:46,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:37:46,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:37:46,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 09:37:46,051] [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
--------------------------------------------------------------------------------
[2023-06-30 09:37:46,054] [INFO] DFAST Taxonomy check result was written to GCA_016708015.1_ASM1670801v1_genomic.fna/tc_result.tsv
[2023-06-30 09:37:46,054] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:37:46,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:37:46,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference/checkm_data
[2023-06-30 09:37:46,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:37:46,102] [INFO] Task started: CheckM
[2023-06-30 09:37:46,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708015.1_ASM1670801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708015.1_ASM1670801v1_genomic.fna/checkm_input GCA_016708015.1_ASM1670801v1_genomic.fna/checkm_result
[2023-06-30 09:38:35,303] [INFO] Task succeeded: CheckM
[2023-06-30 09:38:35,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-30 09:38:35,329] [INFO] ===== Completeness check finished =====
[2023-06-30 09:38:35,329] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:38:35,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708015.1_ASM1670801v1_genomic.fna/markers.fasta)
[2023-06-30 09:38:35,330] [INFO] Task started: Blastn
[2023-06-30 09:38:35,330] [INFO] Running command: blastn -query GCA_016708015.1_ASM1670801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85602c5-3c92-48e9-b8e8-07af6d4adbd8/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708015.1_ASM1670801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:38:36,133] [INFO] Task succeeded: Blastn
[2023-06-30 09:38:36,138] [INFO] Selected 22 target genomes.
[2023-06-30 09:38:36,138] [INFO] Target genome list was writen to GCA_016708015.1_ASM1670801v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:38:36,143] [INFO] Task started: fastANI
[2023-06-30 09:38:36,143] [INFO] Running command: fastANI --query /var/lib/cwl/stga7e65687-b083-46f7-8e3d-70afd7085818/GCA_016708015.1_ASM1670801v1_genomic.fna.gz --refList GCA_016708015.1_ASM1670801v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708015.1_ASM1670801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:38:50,590] [INFO] Task succeeded: fastANI
[2023-06-30 09:38:50,606] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:38:50,606] [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_016709865.1	s__LD21 sp016709865	98.5991	1312	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.60	98.60	0.94	0.94	2	conclusive
GCA_016718875.1	s__LD21 sp016718875	77.9229	244	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715075.1	s__LD21 sp016715075	77.8805	220	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.94	98.94	0.93	0.93	2	-
GCA_903824785.1	s__LD21 sp903824785	77.768	277	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.94	99.93	0.97	0.96	4	-
GCA_003141895.1	s__LD21 sp003141895	77.5633	231	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.95	99.95	0.99	0.99	2	-
GCA_003142255.1	s__LD21 sp003142255	77.458	132	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.86	99.76	0.98	0.97	3	-
GCA_003162595.1	s__LD21 sp003162595	77.4577	184	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141715.1	s__LD21 sp003141715	77.4282	231	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882305.1	s__LD21 sp017882305	77.2846	202	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141415.1	s__LD21 sp003141415	77.1715	244	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319885.1	s__LD21 sp002319885	77.1459	224	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882345.1	s__LD21 sp017882345	77.1032	195	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729475.1	s__LD21 sp012729475	76.8615	69	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003501665.1	s__LD21 sp003501665	76.6013	85	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520925.1	s__LD21 sp003520925	76.4868	131	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.68	99.68	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-30 09:38:50,608] [INFO] GTDB search result was written to GCA_016708015.1_ASM1670801v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:38:50,609] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:38:50,612] [INFO] DFAST_QC result json was written to GCA_016708015.1_ASM1670801v1_genomic.fna/dqc_result.json
[2023-06-30 09:38:50,612] [INFO] DFAST_QC completed!
[2023-06-30 09:38:50,612] [INFO] Total running time: 0h1m46s