[2024-01-25 18:17:05,479] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:17:05,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:17:05,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference
[2024-01-25 18:17:06,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:17:06,614] [INFO] Task started: Prodigal
[2024-01-25 18:17:06,614] [INFO] Running command: gunzip -c /var/lib/cwl/stge3e43f1c-98e1-440d-8a45-6044553006f1/GCF_000169255.2_ASM16925v2_genomic.fna.gz | prodigal -d GCF_000169255.2_ASM16925v2_genomic.fna/cds.fna -a GCF_000169255.2_ASM16925v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:17,917] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:17,917] [INFO] Task started: HMMsearch
[2024-01-25 18:17:17,917] [INFO] Running command: hmmsearch --tblout GCF_000169255.2_ASM16925v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference/reference_markers.hmm GCF_000169255.2_ASM16925v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:18,171] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:18,172] [INFO] Found 6/6 markers.
[2024-01-25 18:17:18,207] [INFO] Query marker FASTA was written to GCF_000169255.2_ASM16925v2_genomic.fna/markers.fasta
[2024-01-25 18:17:18,207] [INFO] Task started: Blastn
[2024-01-25 18:17:18,207] [INFO] Running command: blastn -query GCF_000169255.2_ASM16925v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference/reference_markers.fasta -out GCF_000169255.2_ASM16925v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:18,881] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:18,884] [INFO] Selected 17 target genomes.
[2024-01-25 18:17:18,884] [INFO] Target genome list was writen to GCF_000169255.2_ASM16925v2_genomic.fna/target_genomes.txt
[2024-01-25 18:17:18,897] [INFO] Task started: fastANI
[2024-01-25 18:17:18,897] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e43f1c-98e1-440d-8a45-6044553006f1/GCF_000169255.2_ASM16925v2_genomic.fna.gz --refList GCF_000169255.2_ASM16925v2_genomic.fna/target_genomes.txt --output GCF_000169255.2_ASM16925v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:28,190] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:28,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:28,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:28,198] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:17:28,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:17:28,199] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	82.2096	449	1377	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	81.7122	515	1377	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	81.5985	486	1377	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.5064	274	1377	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	80.4041	151	1377	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	80.1156	152	1377	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.8284	354	1377	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	79.1568	338	1377	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	79.1084	324	1377	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	79.0773	343	1377	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.4426	195	1377	95	below_threshold
Papillibacter cinnamivorans	strain=DSM 12816	GCA_900176335.1	100176	100176	type	True	76.7117	100	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:28,200] [INFO] DFAST Taxonomy check result was written to GCF_000169255.2_ASM16925v2_genomic.fna/tc_result.tsv
[2024-01-25 18:17:28,201] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:28,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:28,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference/checkm_data
[2024-01-25 18:17:28,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:28,243] [INFO] Task started: CheckM
[2024-01-25 18:17:28,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000169255.2_ASM16925v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000169255.2_ASM16925v2_genomic.fna/checkm_input GCF_000169255.2_ASM16925v2_genomic.fna/checkm_result
[2024-01-25 18:18:03,968] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:03,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:03,988] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:03,989] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:03,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000169255.2_ASM16925v2_genomic.fna/markers.fasta)
[2024-01-25 18:18:03,990] [INFO] Task started: Blastn
[2024-01-25 18:18:03,990] [INFO] Running command: blastn -query GCF_000169255.2_ASM16925v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f697dba-3997-41dc-aa8b-0ad071fc9906/dqc_reference/reference_markers_gtdb.fasta -out GCF_000169255.2_ASM16925v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:05,399] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:05,404] [INFO] Selected 14 target genomes.
[2024-01-25 18:18:05,404] [INFO] Target genome list was writen to GCF_000169255.2_ASM16925v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:05,417] [INFO] Task started: fastANI
[2024-01-25 18:18:05,417] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e43f1c-98e1-440d-8a45-6044553006f1/GCF_000169255.2_ASM16925v2_genomic.fna.gz --refList GCF_000169255.2_ASM16925v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000169255.2_ASM16925v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:15,846] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:15,855] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:15,855] [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_000169255.2	s__Pseudoflavonifractor capillosus	100.0	1376	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	95.82	95.81	0.78	0.78	3	conclusive
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	91.4924	684	1377	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_002161215.1	s__Flavonifractor avistercoris	82.9905	562	1377	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_002159265.1	s__Flavonifractor sp002159265	82.9428	518	1377	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_002160305.1	s__Lawsonibacter pullicola	82.5816	420	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.22	97.83	0.90	0.75	8	-
GCF_900626145.1	s__Intestinimonas timonensis	82.4342	462	1377	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_017811815.1	s__Flavonifractor sp017811815	81.9871	497	1377	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_002161085.1	s__Flavonifractor avicola	81.7981	461	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.94	96.68	0.83	0.78	7	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	81.6049	377	1377	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_018711785.1	s__Galloscillospira_A excrementavium	81.5728	319	1377	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_014287675.1	s__Pseudoflavonifractor sp014287675	81.4648	589	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	99.22	99.20	0.93	0.92	18	-
GCA_018715695.1	s__Galloscillospira_A stercoripullorum	81.1996	328	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A	95.0	99.04	99.04	0.82	0.82	2	-
GCA_900549565.1	s__UMGS1202 sp900549565	81.198	453	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287895.1	s__NSJ-51 sp900549795	80.6744	422	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:18:15,857] [INFO] GTDB search result was written to GCF_000169255.2_ASM16925v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:15,858] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:15,861] [INFO] DFAST_QC result json was written to GCF_000169255.2_ASM16925v2_genomic.fna/dqc_result.json
[2024-01-25 18:18:15,861] [INFO] DFAST_QC completed!
[2024-01-25 18:18:15,861] [INFO] Total running time: 0h1m10s