[2023-06-16 22:40:04,673] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:40:04,679] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:40:04,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference
[2023-06-16 22:40:08,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:40:08,092] [INFO] Task started: Prodigal
[2023-06-16 22:40:08,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaa09e7d-909e-4b65-aaa6-c59d7bc58f32/GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna.gz | prodigal -d GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/cds.fna -a GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:40:15,011] [INFO] Task succeeded: Prodigal
[2023-06-16 22:40:15,012] [INFO] Task started: HMMsearch
[2023-06-16 22:40:15,012] [INFO] Running command: hmmsearch --tblout GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference/reference_markers.hmm GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:40:15,271] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:40:15,273] [INFO] Found 6/6 markers.
[2023-06-16 22:40:15,302] [INFO] Query marker FASTA was written to GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/markers.fasta
[2023-06-16 22:40:15,302] [INFO] Task started: Blastn
[2023-06-16 22:40:15,302] [INFO] Running command: blastn -query GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference/reference_markers.fasta -out GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:40:15,952] [INFO] Task succeeded: Blastn
[2023-06-16 22:40:15,958] [INFO] Selected 26 target genomes.
[2023-06-16 22:40:15,958] [INFO] Target genome list was writen to GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/target_genomes.txt
[2023-06-16 22:40:15,966] [INFO] Task started: fastANI
[2023-06-16 22:40:15,967] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa09e7d-909e-4b65-aaa6-c59d7bc58f32/GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna.gz --refList GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/target_genomes.txt --output GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:40:31,001] [INFO] Task succeeded: fastANI
[2023-06-16 22:40:31,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:40:31,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:40:31,022] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-06-16 22:40:31,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 22:40:31,023] [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
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	98.682	773	879	95	conclusive
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.4012	102	879	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	78.4489	64	879	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	77.8366	87	879	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.7061	81	879	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.6691	80	879	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.6445	118	879	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	77.5421	55	879	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.4688	92	879	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	77.3937	96	879	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.3899	90	879	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.3866	86	879	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.3733	121	879	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.3627	120	879	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.3372	112	879	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.3305	117	879	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	77.2763	95	879	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.2556	97	879	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.2489	73	879	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.0074	106	879	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.9556	102	879	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.8694	85	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:40:31,028] [INFO] DFAST Taxonomy check result was written to GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/tc_result.tsv
[2023-06-16 22:40:31,029] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:40:31,029] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:40:31,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference/checkm_data
[2023-06-16 22:40:31,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:40:31,062] [INFO] Task started: CheckM
[2023-06-16 22:40:31,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/checkm_input GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/checkm_result
[2023-06-16 22:40:58,157] [INFO] Task succeeded: CheckM
[2023-06-16 22:40:58,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:40:58,186] [INFO] ===== Completeness check finished =====
[2023-06-16 22:40:58,188] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:40:58,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/markers.fasta)
[2023-06-16 22:40:58,190] [INFO] Task started: Blastn
[2023-06-16 22:40:58,190] [INFO] Running command: blastn -query GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg70dbe7fb-429e-43b9-9a64-e4779dc9222a/dqc_reference/reference_markers_gtdb.fasta -out GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:40:59,235] [INFO] Task succeeded: Blastn
[2023-06-16 22:40:59,240] [INFO] Selected 15 target genomes.
[2023-06-16 22:40:59,240] [INFO] Target genome list was writen to GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:40:59,251] [INFO] Task started: fastANI
[2023-06-16 22:40:59,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa09e7d-909e-4b65-aaa6-c59d7bc58f32/GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna.gz --refList GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/target_genomes_gtdb.txt --output GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:41:07,742] [INFO] Task succeeded: fastANI
[2023-06-16 22:41:07,760] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:41:07,760] [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_000469345.1	s__Eubacterium_I ramulus	98.6564	774	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.54	98.22	0.85	0.78	13	conclusive
GCF_003122485.1	s__Eubacterium_I ramulus_A	85.3146	528	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.76	98.61	0.82	0.80	7	-
GCA_900546495.1	s__Eubacterium_I sp900546495	85.3069	552	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.94	99.87	0.93	0.88	3	-
GCF_001406815.1	s__Agathobacter faecis	79.4012	102	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCA_902362715.1	s__Eubacterium_I sp900066595	77.7962	125	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000225345.1	s__Roseburia hominis	77.6691	80	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_000169235.1	s__Dorea formicigenerans	77.4669	94	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCA_902363825.1	s__CAG-45 sp000438375	77.4049	105	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	-
GCF_900537995.1	s__Roseburia intestinalis	77.3698	121	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCA_900550935.1	s__Roseburia sp900550935	77.1962	78	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCF_003435815.1	s__CAG-317 sp000433215	77.1321	96	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_902782995.1	s__RUG115 sp902782995	77.0187	87	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695765.1	s__VUNI01 sp009695765	77.0074	106	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000174195.1	s__Roseburia inulinivorans	76.9924	102	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCF_014287615.1	s__Blautia sp001304935	76.4926	68	879	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
--------------------------------------------------------------------------------
[2023-06-16 22:41:07,764] [INFO] GTDB search result was written to GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/result_gtdb.tsv
[2023-06-16 22:41:07,764] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:41:07,770] [INFO] DFAST_QC result json was written to GCA_905208265.1_SRR2912781-mag-bin.7_genomic.fna/dqc_result.json
[2023-06-16 22:41:07,770] [INFO] DFAST_QC completed!
[2023-06-16 22:41:07,770] [INFO] Total running time: 0h1m3s