[2023-06-16 23:29:34,285] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:29:34,290] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:29:34,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference
[2023-06-16 23:29:35,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:29:35,582] [INFO] Task started: Prodigal
[2023-06-16 23:29:35,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg280f9203-b410-4717-ae38-78df148411cc/GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna.gz | prodigal -d GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/cds.fna -a GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:29:42,507] [INFO] Task succeeded: Prodigal
[2023-06-16 23:29:42,507] [INFO] Task started: HMMsearch
[2023-06-16 23:29:42,507] [INFO] Running command: hmmsearch --tblout GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference/reference_markers.hmm GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:29:42,718] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:29:42,719] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg280f9203-b410-4717-ae38-78df148411cc/GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna.gz]
[2023-06-16 23:29:42,746] [INFO] Query marker FASTA was written to GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/markers.fasta
[2023-06-16 23:29:42,746] [INFO] Task started: Blastn
[2023-06-16 23:29:42,746] [INFO] Running command: blastn -query GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/markers.fasta -db /var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference/reference_markers.fasta -out GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:29:43,229] [INFO] Task succeeded: Blastn
[2023-06-16 23:29:43,233] [INFO] Selected 14 target genomes.
[2023-06-16 23:29:43,233] [INFO] Target genome list was writen to GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/target_genomes.txt
[2023-06-16 23:29:43,236] [INFO] Task started: fastANI
[2023-06-16 23:29:43,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg280f9203-b410-4717-ae38-78df148411cc/GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna.gz --refList GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/target_genomes.txt --output GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:29:51,971] [INFO] Task succeeded: fastANI
[2023-06-16 23:29:51,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:29:51,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:29:51,984] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:29:51,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 23:29:51,984] [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	89.994	721	955	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	80.5195	268	955	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.4304	269	955	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.8692	345	955	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	79.6617	269	955	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.0124	223	955	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.5337	107	955	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.8131	97	955	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	76.7431	63	955	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.6586	96	955	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.6032	90	955	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.5331	88	955	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.4367	92	955	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	75.7683	51	955	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 23:29:51,987] [INFO] DFAST Taxonomy check result was written to GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/tc_result.tsv
[2023-06-16 23:29:51,988] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:29:51,988] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:29:51,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference/checkm_data
[2023-06-16 23:29:51,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:29:52,020] [INFO] Task started: CheckM
[2023-06-16 23:29:52,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/checkm_input GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/checkm_result
[2023-06-16 23:30:18,339] [INFO] Task succeeded: CheckM
[2023-06-16 23:30:18,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 23:30:18,368] [INFO] ===== Completeness check finished =====
[2023-06-16 23:30:18,369] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:30:18,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/markers.fasta)
[2023-06-16 23:30:18,369] [INFO] Task started: Blastn
[2023-06-16 23:30:18,369] [INFO] Running command: blastn -query GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/markers.fasta -db /var/lib/cwl/stg65bd5e66-b43d-4900-a430-209337456274/dqc_reference/reference_markers_gtdb.fasta -out GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:30:18,833] [INFO] Task succeeded: Blastn
[2023-06-16 23:30:18,837] [INFO] Selected 6 target genomes.
[2023-06-16 23:30:18,837] [INFO] Target genome list was writen to GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:30:18,840] [INFO] Task started: fastANI
[2023-06-16 23:30:18,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg280f9203-b410-4717-ae38-78df148411cc/GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna.gz --refList GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/target_genomes_gtdb.txt --output GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:30:23,495] [INFO] Task succeeded: fastANI
[2023-06-16 23:30:23,502] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:30:23,502] [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_013304735.1	s__Blautia_A sp900066205	98.1382	891	955	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	conclusive
GCF_003461955.1	s__Blautia_A sp900066335	93.6676	780	955	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	-
GCF_001487165.1	s__Blautia_A massiliensis	90.0045	721	955	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	-
GCF_013304825.1	s__Blautia_A schinkii	87.4565	709	955	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	-
GCF_003474435.1	s__Blautia_A sp003474435	87.3923	731	955	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	-
GCA_900764225.1	s__Blautia_A sp900764225	85.6143	512	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:30:23,504] [INFO] GTDB search result was written to GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/result_gtdb.tsv
[2023-06-16 23:30:23,505] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:30:23,509] [INFO] DFAST_QC result json was written to GCA_905200065.1_SRR5519182-mag-bin.19_genomic.fna/dqc_result.json
[2023-06-16 23:30:23,509] [INFO] DFAST_QC completed!
[2023-06-16 23:30:23,509] [INFO] Total running time: 0h0m49s