[2024-01-24 13:57:42,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,852] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference
[2024-01-24 13:57:44,162] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,162] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,163] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e144c3d-2e5e-42ae-8fb0-92fcbf683bfe/GCF_000239295.1_ASM23929v1_genomic.fna.gz | prodigal -d GCF_000239295.1_ASM23929v1_genomic.fna/cds.fna -a GCF_000239295.1_ASM23929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:54,585] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:54,585] [INFO] Task started: HMMsearch
[2024-01-24 13:57:54,585] [INFO] Running command: hmmsearch --tblout GCF_000239295.1_ASM23929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference/reference_markers.hmm GCF_000239295.1_ASM23929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:54,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:54,870] [INFO] Found 6/6 markers.
[2024-01-24 13:57:54,908] [INFO] Query marker FASTA was written to GCF_000239295.1_ASM23929v1_genomic.fna/markers.fasta
[2024-01-24 13:57:54,909] [INFO] Task started: Blastn
[2024-01-24 13:57:54,909] [INFO] Running command: blastn -query GCF_000239295.1_ASM23929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference/reference_markers.fasta -out GCF_000239295.1_ASM23929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,616] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,621] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:55,621] [INFO] Target genome list was writen to GCF_000239295.1_ASM23929v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:55,627] [INFO] Task started: fastANI
[2024-01-24 13:57:55,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e144c3d-2e5e-42ae-8fb0-92fcbf683bfe/GCF_000239295.1_ASM23929v1_genomic.fna.gz --refList GCF_000239295.1_ASM23929v1_genomic.fna/target_genomes.txt --output GCF_000239295.1_ASM23929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:02,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:02,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:02,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:02,982] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:02,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:02,982] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	100.0	1145	1157	95	conclusive
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	99.9718	1156	1157	95	conclusive
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	80.8968	425	1157	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.3321	263	1157	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.6156	312	1157	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	79.2502	333	1157	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	79.2027	325	1157	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.4297	139	1157	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	78.1769	148	1157	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.7998	184	1157	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.4322	102	1157	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.3246	99	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:02,984] [INFO] DFAST Taxonomy check result was written to GCF_000239295.1_ASM23929v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:02,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:02,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:02,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference/checkm_data
[2024-01-24 13:58:02,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:03,026] [INFO] Task started: CheckM
[2024-01-24 13:58:03,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000239295.1_ASM23929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000239295.1_ASM23929v1_genomic.fna/checkm_input GCF_000239295.1_ASM23929v1_genomic.fna/checkm_result
[2024-01-24 13:58:36,862] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:36,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:36,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:36,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000239295.1_ASM23929v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:36,888] [INFO] Task started: Blastn
[2024-01-24 13:58:36,888] [INFO] Running command: blastn -query GCF_000239295.1_ASM23929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg718f2d82-7be5-4d01-b1e6-f94f4d1a34de/dqc_reference/reference_markers_gtdb.fasta -out GCF_000239295.1_ASM23929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:38,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:38,197] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:38,197] [INFO] Target genome list was writen to GCF_000239295.1_ASM23929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:38,211] [INFO] Task started: fastANI
[2024-01-24 13:58:38,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e144c3d-2e5e-42ae-8fb0-92fcbf683bfe/GCF_000239295.1_ASM23929v1_genomic.fna.gz --refList GCF_000239295.1_ASM23929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000239295.1_ASM23929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:48,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:48,175] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:48,176] [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_000239295.1	s__Flavonifractor plautii	100.0	1145	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	conclusive
GCF_002161215.1	s__Flavonifractor avistercoris	86.0339	664	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_900626285.1	s__Flavonifractor massiliensis_A	84.878	583	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159455.1	s__Flavonifractor sp002159455	83.7546	559	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	97.17	96.82	0.76	0.75	4	-
GCA_019119335.1	s__Flavonifractor merdavium	83.5321	487	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159265.1	s__Flavonifractor sp002159265	83.2303	531	1157	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	82.9899	412	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCF_017811815.1	s__Flavonifractor sp017811815	82.921	515	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901955.1	s__Flavonifractor phocaeensis_A	82.6601	464	1157	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_900549565.1	s__UMGS1202 sp900549565	82.2501	486	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711785.1	s__Galloscillospira_A excrementavium	81.1788	293	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A	95.0	98.56	98.56	0.94	0.94	2	-
GCF_002161675.1	s__Enterenecus faecium	79.5392	252	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	96.73	96.16	0.87	0.84	6	-
GCA_905205085.1	s__Lawsonibacter sp900766145	79.0632	232	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.79	99.79	0.87	0.87	2	-
GCA_900543555.1	s__Acutalibacter stercoravium	77.7652	83	1157	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.18	97.66	0.89	0.84	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,178] [INFO] GTDB search result was written to GCF_000239295.1_ASM23929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:48,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:48,181] [INFO] DFAST_QC result json was written to GCF_000239295.1_ASM23929v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:48,182] [INFO] DFAST_QC completed!
[2024-01-24 13:58:48,182] [INFO] Total running time: 0h1m5s