[2024-01-25 20:07:05,471] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:05,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:05,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference
[2024-01-25 20:07:06,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:06,619] [INFO] Task started: Prodigal
[2024-01-25 20:07:06,619] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5ac9d29-8113-4b0f-acbb-92aa348ccc97/GCF_018408575.1_ASM1840857v1_genomic.fna.gz | prodigal -d GCF_018408575.1_ASM1840857v1_genomic.fna/cds.fna -a GCF_018408575.1_ASM1840857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:13,478] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:13,478] [INFO] Task started: HMMsearch
[2024-01-25 20:07:13,478] [INFO] Running command: hmmsearch --tblout GCF_018408575.1_ASM1840857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference/reference_markers.hmm GCF_018408575.1_ASM1840857v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:13,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:13,688] [INFO] Found 6/6 markers.
[2024-01-25 20:07:13,710] [INFO] Query marker FASTA was written to GCF_018408575.1_ASM1840857v1_genomic.fna/markers.fasta
[2024-01-25 20:07:13,711] [INFO] Task started: Blastn
[2024-01-25 20:07:13,711] [INFO] Running command: blastn -query GCF_018408575.1_ASM1840857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference/reference_markers.fasta -out GCF_018408575.1_ASM1840857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:14,349] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:14,352] [INFO] Selected 14 target genomes.
[2024-01-25 20:07:14,352] [INFO] Target genome list was writen to GCF_018408575.1_ASM1840857v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:14,366] [INFO] Task started: fastANI
[2024-01-25 20:07:14,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ac9d29-8113-4b0f-acbb-92aa348ccc97/GCF_018408575.1_ASM1840857v1_genomic.fna.gz --refList GCF_018408575.1_ASM1840857v1_genomic.fna/target_genomes.txt --output GCF_018408575.1_ASM1840857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:23,116] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:23,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:23,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:23,125] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:23,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:23,125] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	100.0	852	852	95	conclusive
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	83.9652	360	852	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	82.2514	70	852	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.6545	261	852	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.9297	153	852	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.0011	216	852	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.5444	89	852	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.179	188	852	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.9906	145	852	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.8281	134	852	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.7884	170	852	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.4143	141	852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:23,128] [INFO] DFAST Taxonomy check result was written to GCF_018408575.1_ASM1840857v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:23,129] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:23,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:23,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference/checkm_data
[2024-01-25 20:07:23,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:23,157] [INFO] Task started: CheckM
[2024-01-25 20:07:23,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018408575.1_ASM1840857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018408575.1_ASM1840857v1_genomic.fna/checkm_input GCF_018408575.1_ASM1840857v1_genomic.fna/checkm_result
[2024-01-25 20:07:47,424] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:47,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:47,440] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:47,441] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:47,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018408575.1_ASM1840857v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:47,441] [INFO] Task started: Blastn
[2024-01-25 20:07:47,441] [INFO] Running command: blastn -query GCF_018408575.1_ASM1840857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82d3c1fb-f4b6-4a7a-88f5-981ff0e744cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018408575.1_ASM1840857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:48,703] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:48,705] [INFO] Selected 16 target genomes.
[2024-01-25 20:07:48,705] [INFO] Target genome list was writen to GCF_018408575.1_ASM1840857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:48,725] [INFO] Task started: fastANI
[2024-01-25 20:07:48,726] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5ac9d29-8113-4b0f-acbb-92aa348ccc97/GCF_018408575.1_ASM1840857v1_genomic.fna.gz --refList GCF_018408575.1_ASM1840857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018408575.1_ASM1840857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:55,652] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:55,662] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:55,662] [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_018408575.1	s__CAG-83 sp000431575	100.0	852	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	conclusive
GCA_018228685.1	s__CAG-83 sp001916855	84.1338	451	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	-
GCA_000435975.1	s__CAG-83 sp000435975	83.4414	344	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	-
GCA_900547745.1	s__CAG-83 sp900547745	81.9958	326	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900551355.1	s__CAG-83 sp900551355	81.8826	274	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900545495.1	s__CAG-83 sp900545495	81.6797	358	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900550585.1	s__CAG-83 sp900550585	81.5552	314	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900548615.1	s__CAG-83 sp900548615	81.5465	298	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.93	97.80	0.81	0.77	3	-
GCA_900545585.1	s__CAG-83 sp900545585	81.4924	353	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_003539495.1	s__CAG-83 sp003539495	80.9474	299	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.87	97.47	0.86	0.82	8	-
GCA_900317425.1	s__CAG-83 sp900317425	80.7129	284	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.98	99.98	0.95	0.95	2	-
GCA_902388735.1	s__CAG-83 sp902388735	80.5767	292	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCA_004557655.1	s__CAG-83 sp004557655	80.5035	252	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313295.1	s__CAG-83 sp900313295	80.3262	210	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	96.38	0.88	0.79	5	-
GCA_017937195.1	s__CAG-83 sp017937195	79.2083	213	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552015.1	s__ER4 sp900552015	77.9633	124	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:55,663] [INFO] GTDB search result was written to GCF_018408575.1_ASM1840857v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:55,664] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:55,667] [INFO] DFAST_QC result json was written to GCF_018408575.1_ASM1840857v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:55,667] [INFO] DFAST_QC completed!
[2024-01-25 20:07:55,667] [INFO] Total running time: 0h0m50s