[2024-01-24 13:27:31,857] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference
[2024-01-24 13:27:33,234] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,235] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg10c86dbe-e7c1-4c4e-bcab-9e7295db6f79/GCF_000307265.1_ASM30726v1_genomic.fna.gz | prodigal -d GCF_000307265.1_ASM30726v1_genomic.fna/cds.fna -a GCF_000307265.1_ASM30726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:42,919] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:42,919] [INFO] Task started: HMMsearch
[2024-01-24 13:27:42,920] [INFO] Running command: hmmsearch --tblout GCF_000307265.1_ASM30726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference/reference_markers.hmm GCF_000307265.1_ASM30726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:43,177] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:43,178] [INFO] Found 6/6 markers.
[2024-01-24 13:27:43,206] [INFO] Query marker FASTA was written to GCF_000307265.1_ASM30726v1_genomic.fna/markers.fasta
[2024-01-24 13:27:43,206] [INFO] Task started: Blastn
[2024-01-24 13:27:43,207] [INFO] Running command: blastn -query GCF_000307265.1_ASM30726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference/reference_markers.fasta -out GCF_000307265.1_ASM30726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:43,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:43,827] [INFO] Selected 9 target genomes.
[2024-01-24 13:27:43,827] [INFO] Target genome list was writen to GCF_000307265.1_ASM30726v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:43,841] [INFO] Task started: fastANI
[2024-01-24 13:27:43,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg10c86dbe-e7c1-4c4e-bcab-9e7295db6f79/GCF_000307265.1_ASM30726v1_genomic.fna.gz --refList GCF_000307265.1_ASM30726v1_genomic.fna/target_genomes.txt --output GCF_000307265.1_ASM30726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:49,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:49,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:49,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:49,015] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:27:49,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:49,015] [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
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	99.9999	1022	1026	95	conclusive
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.4001	265	1026	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.2184	226	1026	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.6694	186	1026	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.4196	138	1026	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.1758	104	1026	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.5699	54	1026	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.5535	89	1026	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.4964	89	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:49,017] [INFO] DFAST Taxonomy check result was written to GCF_000307265.1_ASM30726v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:49,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:49,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:49,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference/checkm_data
[2024-01-24 13:27:49,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:49,053] [INFO] Task started: CheckM
[2024-01-24 13:27:49,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000307265.1_ASM30726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000307265.1_ASM30726v1_genomic.fna/checkm_input GCF_000307265.1_ASM30726v1_genomic.fna/checkm_result
[2024-01-24 13:28:20,592] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:20,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:20,616] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:20,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:20,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000307265.1_ASM30726v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:20,617] [INFO] Task started: Blastn
[2024-01-24 13:28:20,617] [INFO] Running command: blastn -query GCF_000307265.1_ASM30726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5769cafe-57fd-4205-928a-4e298866ab04/dqc_reference/reference_markers_gtdb.fasta -out GCF_000307265.1_ASM30726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:21,531] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:21,535] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:21,535] [INFO] Target genome list was writen to GCF_000307265.1_ASM30726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:21,579] [INFO] Task started: fastANI
[2024-01-24 13:28:21,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg10c86dbe-e7c1-4c4e-bcab-9e7295db6f79/GCF_000307265.1_ASM30726v1_genomic.fna.gz --refList GCF_000307265.1_ASM30726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000307265.1_ASM30726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:37,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:37,380] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:37,380] [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_000307265.1	s__Oscillibacter ruminantium	99.9999	1022	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	98.68	98.68	0.93	0.93	2	conclusive
GCF_000283575.1	s__Oscillibacter valericigenes	82.031	604	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455655.1	s__Oscillibacter sp002455655	81.1264	407	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Oscillibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	78.6569	271	1026	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	78.5502	241	1026	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	78.543	210	1026	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	78.4012	277	1026	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	78.3998	265	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCA_019118935.1	s__Dysosmobacter pullicola	78.346	264	1026	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_900548505.1	s__Dysosmobacter sp900548505	78.2896	222	1026	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	78.1583	227	1026	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_000436875.1	s__Dysosmobacter sp000436875	78.1237	234	1026	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_910587875.1	s__Dysosmobacter sp910587875	77.3933	188	1026	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_902784305.1	s__Onthomonas sp902784305	76.5014	79	1026	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Onthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:37,382] [INFO] GTDB search result was written to GCF_000307265.1_ASM30726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:37,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:37,386] [INFO] DFAST_QC result json was written to GCF_000307265.1_ASM30726v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:37,386] [INFO] DFAST_QC completed!
[2024-01-24 13:28:37,386] [INFO] Total running time: 0h1m6s