[2023-06-19 14:07:07,868] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:07:07,872] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:07:07,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference
[2023-06-19 14:07:09,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:07:09,211] [INFO] Task started: Prodigal
[2023-06-19 14:07:09,212] [INFO] Running command: gunzip -c /var/lib/cwl/stg790c5831-f31b-4d04-a12c-52bca802b091/GCA_018375205.1_ASM1837520v1_genomic.fna.gz | prodigal -d GCA_018375205.1_ASM1837520v1_genomic.fna/cds.fna -a GCA_018375205.1_ASM1837520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:07:16,530] [INFO] Task succeeded: Prodigal
[2023-06-19 14:07:16,531] [INFO] Task started: HMMsearch
[2023-06-19 14:07:16,531] [INFO] Running command: hmmsearch --tblout GCA_018375205.1_ASM1837520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference/reference_markers.hmm GCA_018375205.1_ASM1837520v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:07:16,790] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:07:16,792] [INFO] Found 6/6 markers.
[2023-06-19 14:07:16,824] [INFO] Query marker FASTA was written to GCA_018375205.1_ASM1837520v1_genomic.fna/markers.fasta
[2023-06-19 14:07:16,824] [INFO] Task started: Blastn
[2023-06-19 14:07:16,825] [INFO] Running command: blastn -query GCA_018375205.1_ASM1837520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference/reference_markers.fasta -out GCA_018375205.1_ASM1837520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:17,561] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:17,573] [INFO] Selected 12 target genomes.
[2023-06-19 14:07:17,573] [INFO] Target genome list was writen to GCA_018375205.1_ASM1837520v1_genomic.fna/target_genomes.txt
[2023-06-19 14:07:17,577] [INFO] Task started: fastANI
[2023-06-19 14:07:17,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg790c5831-f31b-4d04-a12c-52bca802b091/GCA_018375205.1_ASM1837520v1_genomic.fna.gz --refList GCA_018375205.1_ASM1837520v1_genomic.fna/target_genomes.txt --output GCA_018375205.1_ASM1837520v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:07:23,932] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:23,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:07:23,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:07:23,945] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:07:23,945] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:07:23,945] [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
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	80.9011	419	821	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	80.9007	404	821	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	80.8938	420	821	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	80.5759	396	821	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	80.57	374	821	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.8553	318	821	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.0915	268	821	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.2725	200	821	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.9873	157	821	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.8182	103	821	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	76.1061	67	821	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.0164	66	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:07:23,950] [INFO] DFAST Taxonomy check result was written to GCA_018375205.1_ASM1837520v1_genomic.fna/tc_result.tsv
[2023-06-19 14:07:23,951] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:07:23,951] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:07:23,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference/checkm_data
[2023-06-19 14:07:23,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:07:23,988] [INFO] Task started: CheckM
[2023-06-19 14:07:23,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018375205.1_ASM1837520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018375205.1_ASM1837520v1_genomic.fna/checkm_input GCA_018375205.1_ASM1837520v1_genomic.fna/checkm_result
[2023-06-19 14:07:50,728] [INFO] Task succeeded: CheckM
[2023-06-19 14:07:50,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.69%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 14:07:50,759] [INFO] ===== Completeness check finished =====
[2023-06-19 14:07:50,759] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:07:50,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018375205.1_ASM1837520v1_genomic.fna/markers.fasta)
[2023-06-19 14:07:50,760] [INFO] Task started: Blastn
[2023-06-19 14:07:50,760] [INFO] Running command: blastn -query GCA_018375205.1_ASM1837520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2becb41b-f4dc-48ba-aadd-d71892858e86/dqc_reference/reference_markers_gtdb.fasta -out GCA_018375205.1_ASM1837520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:52,161] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:52,167] [INFO] Selected 19 target genomes.
[2023-06-19 14:07:52,167] [INFO] Target genome list was writen to GCA_018375205.1_ASM1837520v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:07:52,178] [INFO] Task started: fastANI
[2023-06-19 14:07:52,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg790c5831-f31b-4d04-a12c-52bca802b091/GCA_018375205.1_ASM1837520v1_genomic.fna.gz --refList GCA_018375205.1_ASM1837520v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018375205.1_ASM1837520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:08:02,395] [INFO] Task succeeded: fastANI
[2023-06-19 14:08:02,423] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:08:02,423] [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_001244995.1	s__Intestinimonas massiliensis	99.2439	790	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.15	98.60	0.93	0.82	6	conclusive
GCF_900626145.1	s__Intestinimonas timonensis	81.7508	439	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540545.1	s__Intestinimonas sp900540545	81.7271	466	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119795.1	s__Intestinimonas pullistercoris	81.3947	345	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.29	99.15	0.85	0.82	4	-
GCA_019117605.1	s__Intestinimonas stercoravium	81.296	370	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_019115345.1	s__Intestinimonas stercorigallinarum	81.286	308	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159455.1	s__Flavonifractor sp002159455	81.0974	364	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	97.17	96.82	0.76	0.75	4	-
GCF_004154955.1	s__Intestinimonas butyriciproducens	80.9382	417	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.73	98.09	0.87	0.79	17	-
GCF_900626285.1	s__Flavonifractor massiliensis_A	80.7255	396	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	80.6105	338	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159265.1	s__Flavonifractor sp002159265	80.442	377	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	80.3739	321	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCA_019115785.1	s__Intestinimonas merdavium	80.3216	344	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_002159175.1	s__An92 sp002159175	80.2721	339	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_900544955.1	s__Dysosmobacter sp900544955	78.8256	215	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	78.4035	195	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549885.1	s__Enterenecus sp900549885	78.1875	195	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	98.96	98.96	0.79	0.79	2	-
GCA_000436875.1	s__Dysosmobacter sp000436875	78.0573	152	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.76	95.67	0.88	0.85	3	-
GCA_016293265.1	s__Dysosmobacter sp016293265	77.876	121	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:08:02,425] [INFO] GTDB search result was written to GCA_018375205.1_ASM1837520v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:08:02,426] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:08:02,432] [INFO] DFAST_QC result json was written to GCA_018375205.1_ASM1837520v1_genomic.fna/dqc_result.json
[2023-06-19 14:08:02,432] [INFO] DFAST_QC completed!
[2023-06-19 14:08:02,432] [INFO] Total running time: 0h0m55s