[2023-06-29 12:57:42,368] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:57:42,370] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:57:42,370] [INFO] DQC Reference Directory: /var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference
[2023-06-29 12:57:43,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:57:43,710] [INFO] Task started: Prodigal
[2023-06-29 12:57:43,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1e608ea-ad8f-4294-86c5-6e5141225aa9/GCA_021769425.1_ASM2176942v1_genomic.fna.gz | prodigal -d GCA_021769425.1_ASM2176942v1_genomic.fna/cds.fna -a GCA_021769425.1_ASM2176942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:57:55,509] [INFO] Task succeeded: Prodigal
[2023-06-29 12:57:55,510] [INFO] Task started: HMMsearch
[2023-06-29 12:57:55,510] [INFO] Running command: hmmsearch --tblout GCA_021769425.1_ASM2176942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference/reference_markers.hmm GCA_021769425.1_ASM2176942v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:57:55,822] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:57:55,824] [INFO] Found 6/6 markers.
[2023-06-29 12:57:55,877] [INFO] Query marker FASTA was written to GCA_021769425.1_ASM2176942v1_genomic.fna/markers.fasta
[2023-06-29 12:57:55,877] [INFO] Task started: Blastn
[2023-06-29 12:57:55,877] [INFO] Running command: blastn -query GCA_021769425.1_ASM2176942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference/reference_markers.fasta -out GCA_021769425.1_ASM2176942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:57:56,540] [INFO] Task succeeded: Blastn
[2023-06-29 12:57:56,544] [INFO] Selected 28 target genomes.
[2023-06-29 12:57:56,544] [INFO] Target genome list was writen to GCA_021769425.1_ASM2176942v1_genomic.fna/target_genomes.txt
[2023-06-29 12:57:56,547] [INFO] Task started: fastANI
[2023-06-29 12:57:56,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e608ea-ad8f-4294-86c5-6e5141225aa9/GCA_021769425.1_ASM2176942v1_genomic.fna.gz --refList GCA_021769425.1_ASM2176942v1_genomic.fna/target_genomes.txt --output GCA_021769425.1_ASM2176942v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:58:15,178] [INFO] Task succeeded: fastANI
[2023-06-29 12:58:15,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:58:15,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:58:15,195] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:58:15,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:58:15,196] [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
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.5381	73	1523	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.4704	81	1523	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.4106	75	1523	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	77.115	54	1523	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.9421	87	1523	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.9107	83	1523	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	76.7662	53	1523	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	76.7195	53	1523	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	76.6781	52	1523	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	76.634	52	1523	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.4243	88	1523	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.3032	64	1523	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.292	60	1523	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.252	63	1523	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.2493	58	1523	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	76.2362	58	1523	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.2218	60	1523	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.1938	63	1523	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.1473	86	1523	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.1028	62	1523	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	75.6999	58	1523	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:58:15,199] [INFO] DFAST Taxonomy check result was written to GCA_021769425.1_ASM2176942v1_genomic.fna/tc_result.tsv
[2023-06-29 12:58:15,200] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:58:15,200] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:58:15,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference/checkm_data
[2023-06-29 12:58:15,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:58:15,249] [INFO] Task started: CheckM
[2023-06-29 12:58:15,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021769425.1_ASM2176942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021769425.1_ASM2176942v1_genomic.fna/checkm_input GCA_021769425.1_ASM2176942v1_genomic.fna/checkm_result
[2023-06-29 12:58:53,729] [INFO] Task succeeded: CheckM
[2023-06-29 12:58:53,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:58:53,770] [INFO] ===== Completeness check finished =====
[2023-06-29 12:58:53,771] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:58:53,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021769425.1_ASM2176942v1_genomic.fna/markers.fasta)
[2023-06-29 12:58:53,772] [INFO] Task started: Blastn
[2023-06-29 12:58:53,772] [INFO] Running command: blastn -query GCA_021769425.1_ASM2176942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd493e71a-64cd-46c2-ac07-efe31ca49fba/dqc_reference/reference_markers_gtdb.fasta -out GCA_021769425.1_ASM2176942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:58:54,831] [INFO] Task succeeded: Blastn
[2023-06-29 12:58:54,836] [INFO] Selected 12 target genomes.
[2023-06-29 12:58:54,836] [INFO] Target genome list was writen to GCA_021769425.1_ASM2176942v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:58:54,843] [INFO] Task started: fastANI
[2023-06-29 12:58:54,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1e608ea-ad8f-4294-86c5-6e5141225aa9/GCA_021769425.1_ASM2176942v1_genomic.fna.gz --refList GCA_021769425.1_ASM2176942v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021769425.1_ASM2176942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:59:05,554] [INFO] Task succeeded: fastANI
[2023-06-29 12:59:05,571] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:59:05,572] [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_910575555.1	s__14-2 sp011960065	86.9531	1021	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.61	97.67	0.95	0.76	7	-
GCA_004793545.1	s__14-2 sp004793545	85.4108	989	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584585.1	s__14-2 sp910584585	85.3148	960	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403845.2	s__14-2 sp000403845	80.2026	603	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403255.2	s__14-2 sp000403255	79.8746	611	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.01	99.01	0.96	0.96	2	-
GCA_000403315.2	s__14-2 sp000403315	79.5454	554	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.01	98.74	0.95	0.92	3	-
GCA_910585295.1	s__14-2 sp009774455	79.1814	467	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	99.41	99.41	0.81	0.81	2	-
GCA_910583835.1	s__14-2 sp910583835	77.9378	281	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587895.1	s__14-2 sp910587895	77.7749	236	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000509125.1	s__Clostridium_AP sp000509125	76.6188	60	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.12	98.62	0.95	0.91	5	-
GCF_018785315.1	s__CHH4-2 sp018785315	76.2134	62	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119975.1	s__Blautia merdavium	76.035	69	1523	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:59:05,574] [INFO] GTDB search result was written to GCA_021769425.1_ASM2176942v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:59:05,574] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:59:05,579] [INFO] DFAST_QC result json was written to GCA_021769425.1_ASM2176942v1_genomic.fna/dqc_result.json
[2023-06-29 12:59:05,579] [INFO] DFAST_QC completed!
[2023-06-29 12:59:05,579] [INFO] Total running time: 0h1m23s