[2023-06-13 15:45:10,165] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:10,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:10,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference
[2023-06-13 15:45:11,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:11,605] [INFO] Task started: Prodigal
[2023-06-13 15:45:11,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg184e5f36-2382-44f3-93ad-e19a7d52ee46/GCA_022773065.1_ASM2277306v1_genomic.fna.gz | prodigal -d GCA_022773065.1_ASM2277306v1_genomic.fna/cds.fna -a GCA_022773065.1_ASM2277306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:19,385] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:19,386] [INFO] Task started: HMMsearch
[2023-06-13 15:45:19,386] [INFO] Running command: hmmsearch --tblout GCA_022773065.1_ASM2277306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference/reference_markers.hmm GCA_022773065.1_ASM2277306v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:19,671] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:19,672] [INFO] Found 6/6 markers.
[2023-06-13 15:45:19,706] [INFO] Query marker FASTA was written to GCA_022773065.1_ASM2277306v1_genomic.fna/markers.fasta
[2023-06-13 15:45:19,707] [INFO] Task started: Blastn
[2023-06-13 15:45:19,707] [INFO] Running command: blastn -query GCA_022773065.1_ASM2277306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference/reference_markers.fasta -out GCA_022773065.1_ASM2277306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:20,372] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:20,380] [INFO] Selected 11 target genomes.
[2023-06-13 15:45:20,381] [INFO] Target genome list was writen to GCA_022773065.1_ASM2277306v1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:20,385] [INFO] Task started: fastANI
[2023-06-13 15:45:20,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg184e5f36-2382-44f3-93ad-e19a7d52ee46/GCA_022773065.1_ASM2277306v1_genomic.fna.gz --refList GCA_022773065.1_ASM2277306v1_genomic.fna/target_genomes.txt --output GCA_022773065.1_ASM2277306v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:27,106] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:27,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:27,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:27,118] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:27,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:27,119] [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
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	80.6922	355	831	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.5002	351	831	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	77.9062	218	831	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	77.8337	229	831	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	77.4856	129	831	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	77.2662	127	831	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.1229	141	831	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	76.7766	81	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:27,121] [INFO] DFAST Taxonomy check result was written to GCA_022773065.1_ASM2277306v1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:27,122] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:27,122] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:27,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference/checkm_data
[2023-06-13 15:45:27,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:27,166] [INFO] Task started: CheckM
[2023-06-13 15:45:27,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022773065.1_ASM2277306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022773065.1_ASM2277306v1_genomic.fna/checkm_input GCA_022773065.1_ASM2277306v1_genomic.fna/checkm_result
[2023-06-13 15:45:56,743] [INFO] Task succeeded: CheckM
[2023-06-13 15:45:56,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:45:56,769] [INFO] ===== Completeness check finished =====
[2023-06-13 15:45:56,769] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:45:56,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022773065.1_ASM2277306v1_genomic.fna/markers.fasta)
[2023-06-13 15:45:56,770] [INFO] Task started: Blastn
[2023-06-13 15:45:56,771] [INFO] Running command: blastn -query GCA_022773065.1_ASM2277306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a9c30af-9ce0-4441-a3d6-4cb31e5a402e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022773065.1_ASM2277306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:57,851] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:57,857] [INFO] Selected 9 target genomes.
[2023-06-13 15:45:57,857] [INFO] Target genome list was writen to GCA_022773065.1_ASM2277306v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:45:57,861] [INFO] Task started: fastANI
[2023-06-13 15:45:57,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg184e5f36-2382-44f3-93ad-e19a7d52ee46/GCA_022773065.1_ASM2277306v1_genomic.fna.gz --refList GCA_022773065.1_ASM2277306v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022773065.1_ASM2277306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:03,407] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:03,420] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:46:03,420] [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_900314825.1	s__Selenomonas_C sp900314825	87.3952	607	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	99.95	99.95	0.95	0.95	2	-
GCA_902780535.1	s__Selenomonas_C sp902780535	84.8097	512	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.25	96.14	0.82	0.79	5	-
GCA_900318215.1	s__Selenomonas_C sp900318215	84.38	490	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.85	0.83	0.79	6	-
GCA_900315575.1	s__Selenomonas_C sp900315575	84.3132	529	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.63	0.83	0.78	4	-
GCA_902763085.1	s__Selenomonas_C sp002351185	82.0908	385	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.44	97.41	0.83	0.79	3	-
GCF_000381005.1	s__Selenomonas_C bovis	81.8732	418	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.36	95.92	0.90	0.82	11	-
GCF_000155955.1	s__Mitsuokella multacida	80.6727	357	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.52	96.22	0.92	0.87	5	-
GCF_000702905.1	s__Mitsuokella jalaludinii	80.483	352	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	-
GCA_900770895.1	s__UBA2913 sp900770895	78.0969	185	831	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__UBA2913	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:03,423] [INFO] GTDB search result was written to GCA_022773065.1_ASM2277306v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:03,424] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:03,435] [INFO] DFAST_QC result json was written to GCA_022773065.1_ASM2277306v1_genomic.fna/dqc_result.json
[2023-06-13 15:46:03,436] [INFO] DFAST_QC completed!
[2023-06-13 15:46:03,436] [INFO] Total running time: 0h0m53s