[2023-06-18 14:24:20,317] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:24:20,319] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:24:20,319] [INFO] DQC Reference Directory: /var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference
[2023-06-18 14:24:21,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:24:21,946] [INFO] Task started: Prodigal
[2023-06-18 14:24:21,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg87250cc9-5e42-4714-b1cd-fc6638d65237/GCA_018054945.1_ASM1805494v1_genomic.fna.gz | prodigal -d GCA_018054945.1_ASM1805494v1_genomic.fna/cds.fna -a GCA_018054945.1_ASM1805494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:24:24,984] [INFO] Task succeeded: Prodigal
[2023-06-18 14:24:24,985] [INFO] Task started: HMMsearch
[2023-06-18 14:24:24,985] [INFO] Running command: hmmsearch --tblout GCA_018054945.1_ASM1805494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference/reference_markers.hmm GCA_018054945.1_ASM1805494v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:24:25,217] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:24:25,218] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg87250cc9-5e42-4714-b1cd-fc6638d65237/GCA_018054945.1_ASM1805494v1_genomic.fna.gz]
[2023-06-18 14:24:25,240] [INFO] Query marker FASTA was written to GCA_018054945.1_ASM1805494v1_genomic.fna/markers.fasta
[2023-06-18 14:24:25,241] [INFO] Task started: Blastn
[2023-06-18 14:24:25,241] [INFO] Running command: blastn -query GCA_018054945.1_ASM1805494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference/reference_markers.fasta -out GCA_018054945.1_ASM1805494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:24:25,774] [INFO] Task succeeded: Blastn
[2023-06-18 14:24:25,781] [INFO] Selected 14 target genomes.
[2023-06-18 14:24:25,782] [INFO] Target genome list was writen to GCA_018054945.1_ASM1805494v1_genomic.fna/target_genomes.txt
[2023-06-18 14:24:25,783] [INFO] Task started: fastANI
[2023-06-18 14:24:25,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg87250cc9-5e42-4714-b1cd-fc6638d65237/GCA_018054945.1_ASM1805494v1_genomic.fna.gz --refList GCA_018054945.1_ASM1805494v1_genomic.fna/target_genomes.txt --output GCA_018054945.1_ASM1805494v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:24:33,142] [INFO] Task succeeded: fastANI
[2023-06-18 14:24:33,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:24:33,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:24:33,172] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:24:33,173] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 14:24:33,173] [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
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.8477	77	357	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.7249	78	357	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.6266	79	357	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.6002	82	357	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.3672	50	357	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.0981	55	357	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.926	80	357	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.6842	81	357	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.0794	63	357	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.9974	50	357	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 14:24:33,178] [INFO] DFAST Taxonomy check result was written to GCA_018054945.1_ASM1805494v1_genomic.fna/tc_result.tsv
[2023-06-18 14:24:33,179] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:24:33,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:24:33,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference/checkm_data
[2023-06-18 14:24:33,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:24:33,207] [INFO] Task started: CheckM
[2023-06-18 14:24:33,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054945.1_ASM1805494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054945.1_ASM1805494v1_genomic.fna/checkm_input GCA_018054945.1_ASM1805494v1_genomic.fna/checkm_result
[2023-06-18 14:24:50,668] [INFO] Task succeeded: CheckM
[2023-06-18 14:24:50,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 14:24:50,690] [INFO] ===== Completeness check finished =====
[2023-06-18 14:24:50,690] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:24:50,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054945.1_ASM1805494v1_genomic.fna/markers.fasta)
[2023-06-18 14:24:50,691] [INFO] Task started: Blastn
[2023-06-18 14:24:50,691] [INFO] Running command: blastn -query GCA_018054945.1_ASM1805494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafecd343-1aea-4dd7-8c43-3650022bec50/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054945.1_ASM1805494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:24:51,227] [INFO] Task succeeded: Blastn
[2023-06-18 14:24:51,237] [INFO] Selected 15 target genomes.
[2023-06-18 14:24:51,237] [INFO] Target genome list was writen to GCA_018054945.1_ASM1805494v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:24:51,240] [INFO] Task started: fastANI
[2023-06-18 14:24:51,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg87250cc9-5e42-4714-b1cd-fc6638d65237/GCA_018054945.1_ASM1805494v1_genomic.fna.gz --refList GCA_018054945.1_ASM1805494v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054945.1_ASM1805494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:24:59,491] [INFO] Task succeeded: fastANI
[2023-06-18 14:24:59,504] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:24:59,504] [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_009696065.1	s__Oliverpabstia intestinalis	98.1615	316	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	conclusive
GCF_004123145.1	s__Oliverpabstia faecicola	91.6615	314	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.72	97.58	0.88	0.80	5	-
GCF_013304735.1	s__Blautia_A sp900066205	80.1644	84	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_003461955.1	s__Blautia_A sp900066335	80.0587	78	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCA_004556655.1	s__Oliverpabstia sp004556655	79.3595	110	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018374355.1	s__Oliverpabstia sp018374355	79.0941	108	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013304825.1	s__Blautia_A schinkii	79.0408	71	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCA_000432335.1	s__Oliverpabstia sp000432335	78.9706	108	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.29	99.14	0.86	0.81	5	-
GCF_001487165.1	s__Blautia_A massiliensis	78.8294	75	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.95	95.87	0.85	0.71	55	-
GCA_002361775.1	s__Oliverpabstia sp002361775	78.7065	119	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCF_003474435.1	s__Blautia_A sp003474435	78.6734	78	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.79	98.21	0.92	0.87	5	-
GCF_000153905.1	s__Blautia_A obeum	78.6266	79	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	-
GCF_003477525.1	s__Blautia_A sp003477525	78.2185	81	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCA_003435055.1	s__Marvinbryantia sp900066075	77.9901	60	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	98.92	97.84	0.90	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-18 14:24:59,506] [INFO] GTDB search result was written to GCA_018054945.1_ASM1805494v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:24:59,507] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:24:59,511] [INFO] DFAST_QC result json was written to GCA_018054945.1_ASM1805494v1_genomic.fna/dqc_result.json
[2023-06-18 14:24:59,511] [INFO] DFAST_QC completed!
[2023-06-18 14:24:59,511] [INFO] Total running time: 0h0m39s