[2023-06-29 21:39:21,328] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:39:21,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:39:21,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference
[2023-06-29 21:39:22,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:39:22,608] [INFO] Task started: Prodigal
[2023-06-29 21:39:22,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg242739e9-fde2-44f1-ae3c-83abcdf227e9/GCA_900752865.1_ERS396316_85_genomic.fna.gz | prodigal -d GCA_900752865.1_ERS396316_85_genomic.fna/cds.fna -a GCA_900752865.1_ERS396316_85_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:39:24,268] [INFO] Task succeeded: Prodigal
[2023-06-29 21:39:24,268] [INFO] Task started: HMMsearch
[2023-06-29 21:39:24,269] [INFO] Running command: hmmsearch --tblout GCA_900752865.1_ERS396316_85_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference/reference_markers.hmm GCA_900752865.1_ERS396316_85_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:39:24,469] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:39:24,471] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg242739e9-fde2-44f1-ae3c-83abcdf227e9/GCA_900752865.1_ERS396316_85_genomic.fna.gz]
[2023-06-29 21:39:24,492] [INFO] Query marker FASTA was written to GCA_900752865.1_ERS396316_85_genomic.fna/markers.fasta
[2023-06-29 21:39:24,493] [INFO] Task started: Blastn
[2023-06-29 21:39:24,493] [INFO] Running command: blastn -query GCA_900752865.1_ERS396316_85_genomic.fna/markers.fasta -db /var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference/reference_markers.fasta -out GCA_900752865.1_ERS396316_85_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:39:25,088] [INFO] Task succeeded: Blastn
[2023-06-29 21:39:25,092] [INFO] Selected 17 target genomes.
[2023-06-29 21:39:25,093] [INFO] Target genome list was writen to GCA_900752865.1_ERS396316_85_genomic.fna/target_genomes.txt
[2023-06-29 21:39:25,095] [INFO] Task started: fastANI
[2023-06-29 21:39:25,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg242739e9-fde2-44f1-ae3c-83abcdf227e9/GCA_900752865.1_ERS396316_85_genomic.fna.gz --refList GCA_900752865.1_ERS396316_85_genomic.fna/target_genomes.txt --output GCA_900752865.1_ERS396316_85_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:39:32,057] [INFO] Task succeeded: fastANI
[2023-06-29 21:39:32,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:39:32,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:39:32,060] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:39:32,061] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:39:32,061] [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 21:39:32,063] [INFO] DFAST Taxonomy check result was written to GCA_900752865.1_ERS396316_85_genomic.fna/tc_result.tsv
[2023-06-29 21:39:32,064] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:39:32,064] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:39:32,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference/checkm_data
[2023-06-29 21:39:32,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:39:32,086] [INFO] Task started: CheckM
[2023-06-29 21:39:32,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752865.1_ERS396316_85_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752865.1_ERS396316_85_genomic.fna/checkm_input GCA_900752865.1_ERS396316_85_genomic.fna/checkm_result
[2023-06-29 21:39:45,671] [INFO] Task succeeded: CheckM
[2023-06-29 21:39:45,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:39:45,693] [INFO] ===== Completeness check finished =====
[2023-06-29 21:39:45,693] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:39:45,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752865.1_ERS396316_85_genomic.fna/markers.fasta)
[2023-06-29 21:39:45,694] [INFO] Task started: Blastn
[2023-06-29 21:39:45,694] [INFO] Running command: blastn -query GCA_900752865.1_ERS396316_85_genomic.fna/markers.fasta -db /var/lib/cwl/stg81593a97-4d49-4fd5-a4e1-f007d17be0ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752865.1_ERS396316_85_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:39:46,514] [INFO] Task succeeded: Blastn
[2023-06-29 21:39:46,518] [INFO] Selected 18 target genomes.
[2023-06-29 21:39:46,519] [INFO] Target genome list was writen to GCA_900752865.1_ERS396316_85_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:39:46,523] [INFO] Task started: fastANI
[2023-06-29 21:39:46,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg242739e9-fde2-44f1-ae3c-83abcdf227e9/GCA_900752865.1_ERS396316_85_genomic.fna.gz --refList GCA_900752865.1_ERS396316_85_genomic.fna/target_genomes_gtdb.txt --output GCA_900752865.1_ERS396316_85_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:39:50,499] [INFO] Task succeeded: fastANI
[2023-06-29 21:39:50,522] [INFO] Found 16 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-29 21:39:50,523] [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_905215145.1	s__UMGS872 sp905215145	97.6691	127	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS872	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_900546275.1	s__UMGS872 sp900546275	97.2268	292	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS872	95.0	97.38	97.34	0.83	0.82	3	inconclusive
GCA_900550255.1	s__UBA5026 sp900550255	77.3684	93	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_002425325.1	s__UBA5578 sp002425325	77.3476	81	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059545.1	s__UBA5026 sp015059545	77.2741	115	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059285.1	s__SIG208 sp015059285	77.0475	89	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017459425.1	s__RGIG4382 sp017459425	76.9514	78	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462455.1	s__UMGS1613 sp017462455	76.8278	73	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716405.1	s__Faecisoma merdavium	76.7436	81	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_000432255.1	s__Faecisoma sp000432255	76.6687	80	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	99.02	98.86	0.88	0.87	4	-
GCA_000433675.1	s__CAG-433 sp000433675	76.5185	70	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	97.55	95.67	0.87	0.75	5	-
GCA_904502155.1	s__CAJGDV01 sp904502155	76.4389	65	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAJGDV01	95.0	98.87	97.74	0.85	0.70	3	-
GCA_015059405.1	s__RUG11788 sp015059405	76.3194	55	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773675.1	s__RUG11890 sp902773675	76.3166	71	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11890	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313725.1	s__UBA5026 sp900313725	76.1348	84	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	99.45	98.91	0.94	0.90	3	-
GCA_905211265.1	s__HGM10818 sp905211265	75.7092	61	348	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:39:50,525] [INFO] GTDB search result was written to GCA_900752865.1_ERS396316_85_genomic.fna/result_gtdb.tsv
[2023-06-29 21:39:50,526] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:39:50,531] [INFO] DFAST_QC result json was written to GCA_900752865.1_ERS396316_85_genomic.fna/dqc_result.json
[2023-06-29 21:39:50,532] [INFO] DFAST_QC completed!
[2023-06-29 21:39:50,532] [INFO] Total running time: 0h0m29s