[2023-06-12 22:41:16,786] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:41:16,788] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:41:16,788] [INFO] DQC Reference Directory: /var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference
[2023-06-12 22:41:19,164] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:41:19,165] [INFO] Task started: Prodigal
[2023-06-12 22:41:19,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d05036b-5cda-4e15-a6bc-e6aa70f845b3/GCA_022774655.1_ASM2277465v1_genomic.fna.gz | prodigal -d GCA_022774655.1_ASM2277465v1_genomic.fna/cds.fna -a GCA_022774655.1_ASM2277465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:41:23,744] [INFO] Task succeeded: Prodigal
[2023-06-12 22:41:23,745] [INFO] Task started: HMMsearch
[2023-06-12 22:41:23,745] [INFO] Running command: hmmsearch --tblout GCA_022774655.1_ASM2277465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference/reference_markers.hmm GCA_022774655.1_ASM2277465v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:41:24,004] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:41:24,006] [INFO] Found 6/6 markers.
[2023-06-12 22:41:24,034] [INFO] Query marker FASTA was written to GCA_022774655.1_ASM2277465v1_genomic.fna/markers.fasta
[2023-06-12 22:41:24,035] [INFO] Task started: Blastn
[2023-06-12 22:41:24,035] [INFO] Running command: blastn -query GCA_022774655.1_ASM2277465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference/reference_markers.fasta -out GCA_022774655.1_ASM2277465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:25,244] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:25,249] [INFO] Selected 18 target genomes.
[2023-06-12 22:41:25,250] [INFO] Target genome list was writen to GCA_022774655.1_ASM2277465v1_genomic.fna/target_genomes.txt
[2023-06-12 22:41:25,257] [INFO] Task started: fastANI
[2023-06-12 22:41:25,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d05036b-5cda-4e15-a6bc-e6aa70f845b3/GCA_022774655.1_ASM2277465v1_genomic.fna.gz --refList GCA_022774655.1_ASM2277465v1_genomic.fna/target_genomes.txt --output GCA_022774655.1_ASM2277465v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:41:36,469] [INFO] Task succeeded: fastANI
[2023-06-12 22:41:36,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:41:36,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:41:36,478] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-12 22:41:36,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-12 22:41:36,479] [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
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	98.0718	621	700	95	conclusive
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	98.0212	623	700	95	conclusive
--------------------------------------------------------------------------------
[2023-06-12 22:41:36,481] [INFO] DFAST Taxonomy check result was written to GCA_022774655.1_ASM2277465v1_genomic.fna/tc_result.tsv
[2023-06-12 22:41:36,482] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:41:36,483] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:41:36,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference/checkm_data
[2023-06-12 22:41:36,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:41:36,517] [INFO] Task started: CheckM
[2023-06-12 22:41:36,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022774655.1_ASM2277465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022774655.1_ASM2277465v1_genomic.fna/checkm_input GCA_022774655.1_ASM2277465v1_genomic.fna/checkm_result
[2023-06-12 22:41:57,369] [INFO] Task succeeded: CheckM
[2023-06-12 22:41:57,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:41:57,398] [INFO] ===== Completeness check finished =====
[2023-06-12 22:41:57,398] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:41:57,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022774655.1_ASM2277465v1_genomic.fna/markers.fasta)
[2023-06-12 22:41:57,399] [INFO] Task started: Blastn
[2023-06-12 22:41:57,399] [INFO] Running command: blastn -query GCA_022774655.1_ASM2277465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged064737-82e0-4e14-aa5a-24fb7490ee1e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022774655.1_ASM2277465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:41:58,389] [INFO] Task succeeded: Blastn
[2023-06-12 22:41:58,393] [INFO] Selected 23 target genomes.
[2023-06-12 22:41:58,394] [INFO] Target genome list was writen to GCA_022774655.1_ASM2277465v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:41:58,444] [INFO] Task started: fastANI
[2023-06-12 22:41:58,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d05036b-5cda-4e15-a6bc-e6aa70f845b3/GCA_022774655.1_ASM2277465v1_genomic.fna.gz --refList GCA_022774655.1_ASM2277465v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022774655.1_ASM2277465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:42:09,159] [INFO] Task succeeded: fastANI
[2023-06-12 22:42:09,176] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 22:42:09,176] [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
GCF_000156015.1	s__Butyrivibrio_A crossotus	98.0718	621	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.48	97.83	0.85	0.60	12	conclusive
GCA_016297265.1	s__Butyrivibrio_A sp016297265	78.3361	98	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.79	98.79	0.89	0.89	2	-
GCA_902786515.1	s__UBA2821 sp902786515	78.2312	69	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431815.1	s__Butyrivibrio_A sp000431815	77.9717	159	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.85	98.85	0.94	0.94	3	-
GCA_900768755.1	s__Butyrivibrio_A sp900768755	77.8806	72	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287955.1	s__Lachnospira sp900316325	77.5014	101	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
GCF_003458705.1	s__Lachnospira sp003537285	77.3285	79	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.2525	96	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_002351535.1	s__UBA2821 sp002351535	77.2297	68	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCF_003464165.1	s__Lachnospira sp003451515	77.1234	81	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCA_900545175.1	s__CAG-882 sp900545175	77.0365	76	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	99.03	98.05	0.94	0.87	3	-
GCF_009680455.1	s__Lachnospira eligens_A	76.9991	85	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.6336	97.83	97.23	0.89	0.81	35	-
GCA_900766925.1	s__CAG-127 sp900766925	76.8	50	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551945.1	s__Lachnospira sp900551945	75.8856	59	700	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.31	99.16	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-12 22:42:09,178] [INFO] GTDB search result was written to GCA_022774655.1_ASM2277465v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:42:09,179] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:42:09,182] [INFO] DFAST_QC result json was written to GCA_022774655.1_ASM2277465v1_genomic.fna/dqc_result.json
[2023-06-12 22:42:09,182] [INFO] DFAST_QC completed!
[2023-06-12 22:42:09,182] [INFO] Total running time: 0h0m52s