[2024-01-25 17:45:20,280] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:20,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:20,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference
[2024-01-25 17:45:21,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:21,395] [INFO] Task started: Prodigal
[2024-01-25 17:45:21,395] [INFO] Running command: gunzip -c /var/lib/cwl/stgddfe8ef9-70fa-408a-911b-01995de8925e/GCF_018408705.1_ASM1840870v1_genomic.fna.gz | prodigal -d GCF_018408705.1_ASM1840870v1_genomic.fna/cds.fna -a GCF_018408705.1_ASM1840870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:30,318] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:30,319] [INFO] Task started: HMMsearch
[2024-01-25 17:45:30,319] [INFO] Running command: hmmsearch --tblout GCF_018408705.1_ASM1840870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference/reference_markers.hmm GCF_018408705.1_ASM1840870v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:30,537] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:30,539] [INFO] Found 6/6 markers.
[2024-01-25 17:45:30,569] [INFO] Query marker FASTA was written to GCF_018408705.1_ASM1840870v1_genomic.fna/markers.fasta
[2024-01-25 17:45:30,569] [INFO] Task started: Blastn
[2024-01-25 17:45:30,569] [INFO] Running command: blastn -query GCF_018408705.1_ASM1840870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference/reference_markers.fasta -out GCF_018408705.1_ASM1840870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:31,185] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:31,188] [INFO] Selected 13 target genomes.
[2024-01-25 17:45:31,188] [INFO] Target genome list was writen to GCF_018408705.1_ASM1840870v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:31,235] [INFO] Task started: fastANI
[2024-01-25 17:45:31,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgddfe8ef9-70fa-408a-911b-01995de8925e/GCF_018408705.1_ASM1840870v1_genomic.fna.gz --refList GCF_018408705.1_ASM1840870v1_genomic.fna/target_genomes.txt --output GCF_018408705.1_ASM1840870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:39,558] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:39,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:39,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:39,566] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:39,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:39,567] [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
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	100.0	1134	1134	95	conclusive
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	85.5598	215	1134	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.5073	370	1134	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	80.3938	143	1134	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.0463	156	1134	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.8796	215	1134	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.7615	151	1134	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.1504	135	1134	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.8384	164	1134	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.7315	136	1134	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.439	97	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:39,568] [INFO] DFAST Taxonomy check result was written to GCF_018408705.1_ASM1840870v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:39,568] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:39,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:39,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference/checkm_data
[2024-01-25 17:45:39,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:39,605] [INFO] Task started: CheckM
[2024-01-25 17:45:39,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018408705.1_ASM1840870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018408705.1_ASM1840870v1_genomic.fna/checkm_input GCF_018408705.1_ASM1840870v1_genomic.fna/checkm_result
[2024-01-25 17:46:08,563] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:08,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:08,584] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:08,584] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:08,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018408705.1_ASM1840870v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:08,585] [INFO] Task started: Blastn
[2024-01-25 17:46:08,585] [INFO] Running command: blastn -query GCF_018408705.1_ASM1840870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b2874f5-bfc0-4537-bf90-c4183b3d9150/dqc_reference/reference_markers_gtdb.fasta -out GCF_018408705.1_ASM1840870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:09,765] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:09,769] [INFO] Selected 21 target genomes.
[2024-01-25 17:46:09,769] [INFO] Target genome list was writen to GCF_018408705.1_ASM1840870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:09,792] [INFO] Task started: fastANI
[2024-01-25 17:46:09,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgddfe8ef9-70fa-408a-911b-01995de8925e/GCF_018408705.1_ASM1840870v1_genomic.fna.gz --refList GCF_018408705.1_ASM1840870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018408705.1_ASM1840870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:21,489] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:21,503] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:21,504] [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_018408705.1	s__Dysosmobacter sp014297375	100.0	1133	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.15	98.99	0.84	0.71	5	conclusive
GCA_904393855.1	s__Dysosmobacter sp904393855	80.6833	318	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005121165.2	s__Dysosmobacter welbionis	80.4803	370	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCF_018228705.1	s__Dysosmobacter sp018228705	80.318	388	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	80.0719	356	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCA_900544955.1	s__Dysosmobacter sp900544955	80.0499	319	1134	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_004558115.1	s__Dysosmobacter sp004558115	79.9389	241	1134	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_019118245.1	s__Dysosmobacter excrementigallinarum	79.8424	317	1134	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_019118935.1	s__Dysosmobacter pullicola	79.8122	331	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_019118505.1	s__Dysosmobacter excrementavium	79.8112	306	1134	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	79.5447	314	1134	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_017469475.1	s__Dysosmobacter sp017469475	79.4562	242	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.68	97.62	0.84	0.82	4	-
GCF_000403435.2	s__Dysosmobacter sp000403435	79.4059	343	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.32	98.32	0.80	0.80	2	-
GCA_900551885.1	s__Dysosmobacter sp900551885	79.3861	252	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.92	99.85	0.92	0.84	3	-
GCA_910585385.1	s__Dysosmobacter sp910585385	79.1494	285	1134	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_017937405.1	s__Dysosmobacter sp017937405	79.0174	293	1134	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_910588005.1	s__Dysosmobacter sp910588005	78.7042	244	1134	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_910584075.1	s__Dysosmobacter sp910584075	78.6429	276	1134	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_016293265.1	s__Dysosmobacter sp016293265	78.5642	214	1134	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_015068025.1	s__Dysosmobacter sp015068025	78.5376	179	1134	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_019114165.1	s__An92 sp019114165	76.7396	75	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.69	98.69	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:21,506] [INFO] GTDB search result was written to GCF_018408705.1_ASM1840870v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:21,507] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:21,512] [INFO] DFAST_QC result json was written to GCF_018408705.1_ASM1840870v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:21,513] [INFO] DFAST_QC completed!
[2024-01-25 17:46:21,513] [INFO] Total running time: 0h1m1s