[2024-01-24 13:09:48,950] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:48,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:48,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference
[2024-01-24 13:09:50,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,256] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,257] [INFO] Running command: gunzip -c /var/lib/cwl/stgf30bacd7-4087-479f-8b00-be8b54aadee9/GCF_009696485.1_ASM969648v1_genomic.fna.gz | prodigal -d GCF_009696485.1_ASM969648v1_genomic.fna/cds.fna -a GCF_009696485.1_ASM969648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:57,224] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:57,224] [INFO] Task started: HMMsearch
[2024-01-24 13:09:57,224] [INFO] Running command: hmmsearch --tblout GCF_009696485.1_ASM969648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference/reference_markers.hmm GCF_009696485.1_ASM969648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:57,475] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:57,476] [INFO] Found 6/6 markers.
[2024-01-24 13:09:57,507] [INFO] Query marker FASTA was written to GCF_009696485.1_ASM969648v1_genomic.fna/markers.fasta
[2024-01-24 13:09:57,507] [INFO] Task started: Blastn
[2024-01-24 13:09:57,507] [INFO] Running command: blastn -query GCF_009696485.1_ASM969648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference/reference_markers.fasta -out GCF_009696485.1_ASM969648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:58,106] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:58,110] [INFO] Selected 25 target genomes.
[2024-01-24 13:09:58,110] [INFO] Target genome list was writen to GCF_009696485.1_ASM969648v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:58,186] [INFO] Task started: fastANI
[2024-01-24 13:09:58,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30bacd7-4087-479f-8b00-be8b54aadee9/GCF_009696485.1_ASM969648v1_genomic.fna.gz --refList GCF_009696485.1_ASM969648v1_genomic.fna/target_genomes.txt --output GCF_009696485.1_ASM969648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:11,475] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:11,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:11,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:11,492] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:11,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:11,493] [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
Suipraeoptans intestinalis	strain=68-1-5	GCA_009696485.1	2606628	2606628	type	True	100.0	838	841	95	conclusive
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	82.127	99	841	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.5863	77	841	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	80.1106	89	841	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.4031	75	841	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	78.7439	120	841	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.6701	85	841	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.6437	88	841	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.4732	52	841	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.3987	84	841	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	78.3679	128	841	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	78.303	52	841	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	78.0116	63	841	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.9515	81	841	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.9456	60	841	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:11,494] [INFO] DFAST Taxonomy check result was written to GCF_009696485.1_ASM969648v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:11,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:11,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:11,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference/checkm_data
[2024-01-24 13:10:11,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:11,523] [INFO] Task started: CheckM
[2024-01-24 13:10:11,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696485.1_ASM969648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696485.1_ASM969648v1_genomic.fna/checkm_input GCF_009696485.1_ASM969648v1_genomic.fna/checkm_result
[2024-01-24 13:10:37,684] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:37,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.06%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:37,710] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:37,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:37,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696485.1_ASM969648v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:37,711] [INFO] Task started: Blastn
[2024-01-24 13:10:37,711] [INFO] Running command: blastn -query GCF_009696485.1_ASM969648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb231575c-2db7-4e78-b921-529188bfcdfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696485.1_ASM969648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:38,507] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:38,510] [INFO] Selected 28 target genomes.
[2024-01-24 13:10:38,510] [INFO] Target genome list was writen to GCF_009696485.1_ASM969648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:38,684] [INFO] Task started: fastANI
[2024-01-24 13:10:38,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30bacd7-4087-479f-8b00-be8b54aadee9/GCF_009696485.1_ASM969648v1_genomic.fna.gz --refList GCF_009696485.1_ASM969648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696485.1_ASM969648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:52,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:52,489] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:52,489] [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_009696485.1	s__Suipraeoptans intestinalis	100.0	838	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Suipraeoptans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	82.0454	97	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A	95.0	98.15	98.07	0.82	0.80	5	-
GCA_000155875.1	s__Bariatricus comes	81.1428	74	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_900312975.1	s__Massilistercora timonensis	78.7439	120	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	95.86	95.52	0.90	0.88	4	-
GCF_003435815.1	s__CAG-317 sp000433215	78.7434	82	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCF_016901695.1	s__Lachnoclostridium_B massiliensis_A	78.4306	81	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001754075.1	s__Merdimonas faecis	78.3641	127	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	98.52	97.96	0.90	0.84	10	-
GCA_910574285.1	s__Sporofaciens sp009774295	78.344	96	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.51	98.02	0.91	0.84	4	-
GCF_000765215.1	s__Lachnoclostridium_B sp000765215	78.3381	104	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.26	97.36	0.89	0.84	10	-
GCF_016902415.1	s__Merdimonas massiliensis	78.2603	124	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	97.93	97.91	0.86	0.83	3	-
GCF_002160985.1	s__Lachnoclostridium_B stercoravium	77.933	97	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.37	98.26	0.93	0.92	3	-
GCA_910574715.1	s__Sporofaciens sp910574715	77.7988	93	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.89	98.89	0.95	0.95	2	-
GCA_910575475.1	s__Schaedlerella sp910575475	77.6384	92	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.35	99.35	0.93	0.93	2	-
GCA_910575835.1	s__Sporofaciens sp910575835	77.5476	106	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578865.1	s__CAG-317 sp011960265	77.5004	97	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	99.18	99.18	0.88	0.88	2	-
GCA_904419285.1	s__Mediterraneibacter caccogallinarum	77.2703	53	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.44	97.89	0.90	0.83	10	-
GCA_910585725.1	s__Sporofaciens sp910585725	77.028	70	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295505.1	s__Dorea_A sp016295505	76.8734	50	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579015.1	s__Sporofaciens sp910579015	76.8336	79	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120575.1	s__Mediterraneibacter quadrami	76.3056	57	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:52,491] [INFO] GTDB search result was written to GCF_009696485.1_ASM969648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:52,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:52,496] [INFO] DFAST_QC result json was written to GCF_009696485.1_ASM969648v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:52,496] [INFO] DFAST_QC completed!
[2024-01-24 13:10:52,496] [INFO] Total running time: 0h1m4s