[2023-06-29 16:46:59,269] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:46:59,271] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:46:59,271] [INFO] DQC Reference Directory: /var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference
[2023-06-29 16:47:00,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:47:00,481] [INFO] Task started: Prodigal
[2023-06-29 16:47:00,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b0a52a6-5d31-40f5-a263-74e0719a6a07/GCA_023708565.1_ASM2370856v1_genomic.fna.gz | prodigal -d GCA_023708565.1_ASM2370856v1_genomic.fna/cds.fna -a GCA_023708565.1_ASM2370856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:47:10,459] [INFO] Task succeeded: Prodigal
[2023-06-29 16:47:10,459] [INFO] Task started: HMMsearch
[2023-06-29 16:47:10,460] [INFO] Running command: hmmsearch --tblout GCA_023708565.1_ASM2370856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference/reference_markers.hmm GCA_023708565.1_ASM2370856v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:47:10,714] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:47:10,715] [INFO] Found 6/6 markers.
[2023-06-29 16:47:10,762] [INFO] Query marker FASTA was written to GCA_023708565.1_ASM2370856v1_genomic.fna/markers.fasta
[2023-06-29 16:47:10,762] [INFO] Task started: Blastn
[2023-06-29 16:47:10,763] [INFO] Running command: blastn -query GCA_023708565.1_ASM2370856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference/reference_markers.fasta -out GCA_023708565.1_ASM2370856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:11,452] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:11,456] [INFO] Selected 24 target genomes.
[2023-06-29 16:47:11,456] [INFO] Target genome list was writen to GCA_023708565.1_ASM2370856v1_genomic.fna/target_genomes.txt
[2023-06-29 16:47:11,458] [INFO] Task started: fastANI
[2023-06-29 16:47:11,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0a52a6-5d31-40f5-a263-74e0719a6a07/GCA_023708565.1_ASM2370856v1_genomic.fna.gz --refList GCA_023708565.1_ASM2370856v1_genomic.fna/target_genomes.txt --output GCA_023708565.1_ASM2370856v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:47:22,444] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:22,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:47:22,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:47:22,456] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:47:22,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:47:22,456] [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	79.531	130	1142	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	79.0632	62	1142	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	79.0632	62	1142	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.313	94	1142	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.9007	121	1142	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.649	85	1142	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.5912	85	1142	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.5636	102	1142	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	77.4888	87	1142	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.2442	100	1142	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.0911	91	1142	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.8502	99	1142	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.6149	79	1142	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:47:22,458] [INFO] DFAST Taxonomy check result was written to GCA_023708565.1_ASM2370856v1_genomic.fna/tc_result.tsv
[2023-06-29 16:47:22,459] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:47:22,459] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:47:22,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference/checkm_data
[2023-06-29 16:47:22,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:47:22,500] [INFO] Task started: CheckM
[2023-06-29 16:47:22,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708565.1_ASM2370856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708565.1_ASM2370856v1_genomic.fna/checkm_input GCA_023708565.1_ASM2370856v1_genomic.fna/checkm_result
[2023-06-29 16:47:55,914] [INFO] Task succeeded: CheckM
[2023-06-29 16:47:55,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:47:55,937] [INFO] ===== Completeness check finished =====
[2023-06-29 16:47:55,938] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:47:55,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708565.1_ASM2370856v1_genomic.fna/markers.fasta)
[2023-06-29 16:47:55,938] [INFO] Task started: Blastn
[2023-06-29 16:47:55,939] [INFO] Running command: blastn -query GCA_023708565.1_ASM2370856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf434bf50-3dea-4314-98cc-81365841c9fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708565.1_ASM2370856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:57,172] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:57,177] [INFO] Selected 11 target genomes.
[2023-06-29 16:47:57,177] [INFO] Target genome list was writen to GCA_023708565.1_ASM2370856v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:47:57,179] [INFO] Task started: fastANI
[2023-06-29 16:47:57,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0a52a6-5d31-40f5-a263-74e0719a6a07/GCA_023708565.1_ASM2370856v1_genomic.fna.gz --refList GCA_023708565.1_ASM2370856v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708565.1_ASM2370856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:48:03,501] [INFO] Task succeeded: fastANI
[2023-06-29 16:48:03,514] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:48:03,515] [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
GCA_000434635.1	s__Faecousia sp000434635	97.0132	615	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.30	97.16	0.81	0.81	4	conclusive
GCA_900546075.1	s__Faecousia sp900546075	93.1106	515	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.06	96.74	0.84	0.78	6	-
GCA_002436765.1	s__Faecousia sp002436765	91.5944	496	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_004562395.1	s__Faecousia sp004562395	81.3305	280	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437585.1	s__Faecousia sp002437585	80.816	324	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_900544945.1	s__Faecousia sp900544945	80.8144	316	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_004555705.1	s__Faecousia sp004555705	80.1265	270	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461445.1	s__Faecousia sp017461445	80.1029	327	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900763965.1	s__Faecousia sp900763965	79.846	238	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398105.1	s__Faecousia sp017398105	79.5679	273	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770015.1	s__Faecousia sp900770015	78.9845	234	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:48:03,517] [INFO] GTDB search result was written to GCA_023708565.1_ASM2370856v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:48:03,517] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:48:03,521] [INFO] DFAST_QC result json was written to GCA_023708565.1_ASM2370856v1_genomic.fna/dqc_result.json
[2023-06-29 16:48:03,521] [INFO] DFAST_QC completed!
[2023-06-29 16:48:03,521] [INFO] Total running time: 0h1m4s