[2023-06-17 16:36:40,253] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:36:40,255] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:36:40,255] [INFO] DQC Reference Directory: /var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference
[2023-06-17 16:36:41,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:36:41,565] [INFO] Task started: Prodigal
[2023-06-17 16:36:41,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb722951-42b0-4091-b640-ed9e2094893d/GCA_003155195.1_20120600_S2S_genomic.fna.gz | prodigal -d GCA_003155195.1_20120600_S2S_genomic.fna/cds.fna -a GCA_003155195.1_20120600_S2S_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:36:47,518] [INFO] Task succeeded: Prodigal
[2023-06-17 16:36:47,518] [INFO] Task started: HMMsearch
[2023-06-17 16:36:47,519] [INFO] Running command: hmmsearch --tblout GCA_003155195.1_20120600_S2S_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference/reference_markers.hmm GCA_003155195.1_20120600_S2S_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:36:47,751] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:36:47,752] [INFO] Found 6/6 markers.
[2023-06-17 16:36:47,797] [INFO] Query marker FASTA was written to GCA_003155195.1_20120600_S2S_genomic.fna/markers.fasta
[2023-06-17 16:36:47,798] [INFO] Task started: Blastn
[2023-06-17 16:36:47,798] [INFO] Running command: blastn -query GCA_003155195.1_20120600_S2S_genomic.fna/markers.fasta -db /var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference/reference_markers.fasta -out GCA_003155195.1_20120600_S2S_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:36:48,519] [INFO] Task succeeded: Blastn
[2023-06-17 16:36:48,524] [INFO] Selected 27 target genomes.
[2023-06-17 16:36:48,524] [INFO] Target genome list was writen to GCA_003155195.1_20120600_S2S_genomic.fna/target_genomes.txt
[2023-06-17 16:36:48,525] [INFO] Task started: fastANI
[2023-06-17 16:36:48,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb722951-42b0-4091-b640-ed9e2094893d/GCA_003155195.1_20120600_S2S_genomic.fna.gz --refList GCA_003155195.1_20120600_S2S_genomic.fna/target_genomes.txt --output GCA_003155195.1_20120600_S2S_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:37:08,203] [INFO] Task succeeded: fastANI
[2023-06-17 16:37:08,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:37:08,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:37:08,208] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:37:08,208] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:37:08,208] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.5447	55	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:37:08,211] [INFO] DFAST Taxonomy check result was written to GCA_003155195.1_20120600_S2S_genomic.fna/tc_result.tsv
[2023-06-17 16:37:08,211] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:37:08,211] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:37:08,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference/checkm_data
[2023-06-17 16:37:08,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:37:08,241] [INFO] Task started: CheckM
[2023-06-17 16:37:08,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003155195.1_20120600_S2S_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003155195.1_20120600_S2S_genomic.fna/checkm_input GCA_003155195.1_20120600_S2S_genomic.fna/checkm_result
[2023-06-17 16:37:31,693] [INFO] Task succeeded: CheckM
[2023-06-17 16:37:31,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:37:31,720] [INFO] ===== Completeness check finished =====
[2023-06-17 16:37:31,720] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:37:31,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003155195.1_20120600_S2S_genomic.fna/markers.fasta)
[2023-06-17 16:37:31,721] [INFO] Task started: Blastn
[2023-06-17 16:37:31,721] [INFO] Running command: blastn -query GCA_003155195.1_20120600_S2S_genomic.fna/markers.fasta -db /var/lib/cwl/stga266ba91-fbe2-42b9-b095-67abe0ef3434/dqc_reference/reference_markers_gtdb.fasta -out GCA_003155195.1_20120600_S2S_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:37:32,576] [INFO] Task succeeded: Blastn
[2023-06-17 16:37:32,580] [INFO] Selected 16 target genomes.
[2023-06-17 16:37:32,580] [INFO] Target genome list was writen to GCA_003155195.1_20120600_S2S_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:37:32,582] [INFO] Task started: fastANI
[2023-06-17 16:37:32,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb722951-42b0-4091-b640-ed9e2094893d/GCA_003155195.1_20120600_S2S_genomic.fna.gz --refList GCA_003155195.1_20120600_S2S_genomic.fna/target_genomes_gtdb.txt --output GCA_003155195.1_20120600_S2S_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:37:39,656] [INFO] Task succeeded: fastANI
[2023-06-17 16:37:39,670] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:37:39,670] [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_003160115.1	s__RAAP-2 sp003160115	99.6935	557	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.36	95.42	0.89	0.81	14	conclusive
GCA_003133125.1	s__RAAP-2 sp003133125	82.0191	391	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.58	99.35	0.91	0.88	7	-
GCA_003163875.1	s__RAAP-2 sp003163875	79.0477	193	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883045.1	s__RAAP-2 sp017883045	79.0389	245	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158855.1	s__RAAP-2 sp003158855	78.8799	261	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138815.1	s__RAAP-2 sp003138815	78.8318	248	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.69	0.94	0.86	28	-
GCA_003132205.1	s__RAAP-2 sp003132205	78.7585	261	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170315.1	s__RAAP-2 sp003170315	78.4083	177	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136495.1	s__RAAP-2 sp003136495	78.3437	173	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.28	99.03	0.82	0.81	5	-
GCA_003133665.1	s__RAAP-2 sp003133665	78.2392	208	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133685.1	s__RAAP-2 sp003133685	77.9721	198	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	98.41	97.01	0.93	0.87	3	-
GCA_003141095.1	s__RAAP-2 sp003141095	77.9417	230	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.73	99.55	0.93	0.91	10	-
GCA_003168075.1	s__RAAP-2 sp003168075	77.8876	139	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.34	99.34	0.88	0.88	2	-
GCA_003132305.1	s__RAAP-2 sp003132305	77.746	174	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.79	0.98	0.97	7	-
GCA_003152555.1	s__RAAP-2 sp003152555	77.1763	128	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	98.42	98.38	0.78	0.75	3	-
GCA_903828785.1	s__RAAP-2 sp903828785	76.7873	59	647	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-17 16:37:39,672] [INFO] GTDB search result was written to GCA_003155195.1_20120600_S2S_genomic.fna/result_gtdb.tsv
[2023-06-17 16:37:39,673] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:37:39,676] [INFO] DFAST_QC result json was written to GCA_003155195.1_20120600_S2S_genomic.fna/dqc_result.json
[2023-06-17 16:37:39,676] [INFO] DFAST_QC completed!
[2023-06-17 16:37:39,676] [INFO] Total running time: 0h0m59s