[2024-01-25 18:56:20,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:20,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:20,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference
[2024-01-25 18:56:21,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:21,721] [INFO] Task started: Prodigal
[2024-01-25 18:56:21,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg0174e486-fe28-44b1-9792-43398cda0251/GCF_025567005.1_ASM2556700v1_genomic.fna.gz | prodigal -d GCF_025567005.1_ASM2556700v1_genomic.fna/cds.fna -a GCF_025567005.1_ASM2556700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:28,722] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:28,722] [INFO] Task started: HMMsearch
[2024-01-25 18:56:28,723] [INFO] Running command: hmmsearch --tblout GCF_025567005.1_ASM2556700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference/reference_markers.hmm GCF_025567005.1_ASM2556700v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:28,984] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:28,985] [INFO] Found 6/6 markers.
[2024-01-25 18:56:29,012] [INFO] Query marker FASTA was written to GCF_025567005.1_ASM2556700v1_genomic.fna/markers.fasta
[2024-01-25 18:56:29,013] [INFO] Task started: Blastn
[2024-01-25 18:56:29,013] [INFO] Running command: blastn -query GCF_025567005.1_ASM2556700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference/reference_markers.fasta -out GCF_025567005.1_ASM2556700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:29,692] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:29,695] [INFO] Selected 24 target genomes.
[2024-01-25 18:56:29,695] [INFO] Target genome list was writen to GCF_025567005.1_ASM2556700v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:29,711] [INFO] Task started: fastANI
[2024-01-25 18:56:29,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg0174e486-fe28-44b1-9792-43398cda0251/GCF_025567005.1_ASM2556700v1_genomic.fna.gz --refList GCF_025567005.1_ASM2556700v1_genomic.fna/target_genomes.txt --output GCF_025567005.1_ASM2556700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:43,915] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:43,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:43,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:43,928] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:56:43,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:56:43,928] [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
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	84.9521	692	1068	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	81.3991	147	1068	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	80.0131	82	1068	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.9316	152	1068	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	79.5216	148	1068	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	79.3679	108	1068	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.2909	152	1068	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.2241	150	1068	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.147	110	1068	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	78.8914	159	1068	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.5288	69	1068	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	78.1228	81	1068	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	78.0618	68	1068	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.9185	119	1068	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	77.8692	115	1068	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.694	113	1068	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.6912	83	1068	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.3284	78	1068	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.2164	56	1068	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.2585	50	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:43,930] [INFO] DFAST Taxonomy check result was written to GCF_025567005.1_ASM2556700v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:43,930] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:43,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:43,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference/checkm_data
[2024-01-25 18:56:43,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:43,965] [INFO] Task started: CheckM
[2024-01-25 18:56:43,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567005.1_ASM2556700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567005.1_ASM2556700v1_genomic.fna/checkm_input GCF_025567005.1_ASM2556700v1_genomic.fna/checkm_result
[2024-01-25 18:57:09,377] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:09,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:09,392] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:09,392] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:09,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567005.1_ASM2556700v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:09,392] [INFO] Task started: Blastn
[2024-01-25 18:57:09,392] [INFO] Running command: blastn -query GCF_025567005.1_ASM2556700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1736df2-d491-4af1-988c-1ed02c40e3fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567005.1_ASM2556700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:10,433] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:10,436] [INFO] Selected 15 target genomes.
[2024-01-25 18:57:10,436] [INFO] Target genome list was writen to GCF_025567005.1_ASM2556700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:10,457] [INFO] Task started: fastANI
[2024-01-25 18:57:10,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg0174e486-fe28-44b1-9792-43398cda0251/GCF_025567005.1_ASM2556700v1_genomic.fna.gz --refList GCF_025567005.1_ASM2556700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567005.1_ASM2556700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:18,732] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:18,742] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:18,742] [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_003435055.1	s__Marvinbryantia sp900066075	97.8434	852	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	98.92	97.84	0.90	0.80	3	conclusive
GCA_900544685.1	s__Marvinbryantia sp900544685	84.9795	642	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385005.1	s__Marvinbryantia sp014385005	84.9371	693	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	98.94	98.94	0.98	0.98	2	-
GCF_009696065.1	s__Oliverpabstia intestinalis	80.5426	151	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
GCF_013300725.1	s__Bariatricus comes_A	80.3446	121	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_018223385.1	s__JAGTTR01 sp018223385	79.0049	66	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGTTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539525.1	s__CAG-56 sp900539525	78.009	112	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.91	99.91	0.93	0.93	2	-
GCA_016297895.1	s__Marvinbryantia sp016297895	78.0006	163	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361955.1	s__CAG-56 sp002361955	77.4979	74	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.90	99.85	0.92	0.90	5	-
GCF_012524165.2	s__Muricomes sp012524165	77.3646	77	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441865.1	s__CAG-194 sp002441865	77.1465	60	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	99.31	99.31	0.87	0.87	2	-
GCF_018917935.1	s__CAG-194 sp018917935	77.0365	75	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214675.1	s__UMGS1375 sp905214675	76.9431	89	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112635.1	s__Blautia_A intestinigallinarum	76.6373	56	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.75	99.75	0.95	0.95	2	-
GCA_018713105.1	s__Limivivens merdigallinarum	76.3716	59	1068	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.32	98.32	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:18,743] [INFO] GTDB search result was written to GCF_025567005.1_ASM2556700v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:18,745] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:18,750] [INFO] DFAST_QC result json was written to GCF_025567005.1_ASM2556700v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:18,750] [INFO] DFAST_QC completed!
[2024-01-25 18:57:18,750] [INFO] Total running time: 0h0m58s