[2023-06-05 23:02:21,082] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:02:21,084] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:02:21,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference
[2023-06-05 23:02:22,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:02:22,294] [INFO] Task started: Prodigal
[2023-06-05 23:02:22,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d889a6e-8fa9-4cad-8551-00c339bc0ef3/GCA_934403785.1_ERR7745545_bin.146_genomic.fna.gz | prodigal -d GCA_934403785.1_ERR7745545_bin.146_genomic.fna/cds.fna -a GCA_934403785.1_ERR7745545_bin.146_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:02:26,058] [INFO] Task succeeded: Prodigal
[2023-06-05 23:02:26,059] [INFO] Task started: HMMsearch
[2023-06-05 23:02:26,059] [INFO] Running command: hmmsearch --tblout GCA_934403785.1_ERR7745545_bin.146_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference/reference_markers.hmm GCA_934403785.1_ERR7745545_bin.146_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:02:26,272] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:02:26,273] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7d889a6e-8fa9-4cad-8551-00c339bc0ef3/GCA_934403785.1_ERR7745545_bin.146_genomic.fna.gz]
[2023-06-05 23:02:26,290] [INFO] Query marker FASTA was written to GCA_934403785.1_ERR7745545_bin.146_genomic.fna/markers.fasta
[2023-06-05 23:02:26,290] [INFO] Task started: Blastn
[2023-06-05 23:02:26,290] [INFO] Running command: blastn -query GCA_934403785.1_ERR7745545_bin.146_genomic.fna/markers.fasta -db /var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference/reference_markers.fasta -out GCA_934403785.1_ERR7745545_bin.146_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:02:26,847] [INFO] Task succeeded: Blastn
[2023-06-05 23:02:26,851] [INFO] Selected 16 target genomes.
[2023-06-05 23:02:26,851] [INFO] Target genome list was writen to GCA_934403785.1_ERR7745545_bin.146_genomic.fna/target_genomes.txt
[2023-06-05 23:02:26,855] [INFO] Task started: fastANI
[2023-06-05 23:02:26,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d889a6e-8fa9-4cad-8551-00c339bc0ef3/GCA_934403785.1_ERR7745545_bin.146_genomic.fna.gz --refList GCA_934403785.1_ERR7745545_bin.146_genomic.fna/target_genomes.txt --output GCA_934403785.1_ERR7745545_bin.146_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:02:35,507] [INFO] Task succeeded: fastANI
[2023-06-05 23:02:35,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:02:35,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:02:35,516] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:02:35,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 23:02:35,516] [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	83.7051	340	571	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	79.5126	152	571	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.3991	150	571	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	79.3247	150	571	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	78.9918	184	571	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	78.9199	187	571	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	78.8505	179	571	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.6629	138	571	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.5466	51	571	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.5388	51	571	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 23:02:35,520] [INFO] DFAST Taxonomy check result was written to GCA_934403785.1_ERR7745545_bin.146_genomic.fna/tc_result.tsv
[2023-06-05 23:02:35,520] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:02:35,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:02:35,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference/checkm_data
[2023-06-05 23:02:35,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:02:35,548] [INFO] Task started: CheckM
[2023-06-05 23:02:35,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934403785.1_ERR7745545_bin.146_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934403785.1_ERR7745545_bin.146_genomic.fna/checkm_input GCA_934403785.1_ERR7745545_bin.146_genomic.fna/checkm_result
[2023-06-05 23:02:52,625] [INFO] Task succeeded: CheckM
[2023-06-05 23:02:52,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:02:52,640] [INFO] ===== Completeness check finished =====
[2023-06-05 23:02:52,640] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:02:52,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934403785.1_ERR7745545_bin.146_genomic.fna/markers.fasta)
[2023-06-05 23:02:52,641] [INFO] Task started: Blastn
[2023-06-05 23:02:52,641] [INFO] Running command: blastn -query GCA_934403785.1_ERR7745545_bin.146_genomic.fna/markers.fasta -db /var/lib/cwl/stg256547b6-dcd0-4949-8784-0c2fa22db556/dqc_reference/reference_markers_gtdb.fasta -out GCA_934403785.1_ERR7745545_bin.146_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:02:53,527] [INFO] Task succeeded: Blastn
[2023-06-05 23:02:53,530] [INFO] Selected 7 target genomes.
[2023-06-05 23:02:53,530] [INFO] Target genome list was writen to GCA_934403785.1_ERR7745545_bin.146_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:02:53,533] [INFO] Task started: fastANI
[2023-06-05 23:02:53,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d889a6e-8fa9-4cad-8551-00c339bc0ef3/GCA_934403785.1_ERR7745545_bin.146_genomic.fna.gz --refList GCA_934403785.1_ERR7745545_bin.146_genomic.fna/target_genomes_gtdb.txt --output GCA_934403785.1_ERR7745545_bin.146_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:02:58,007] [INFO] Task succeeded: fastANI
[2023-06-05 23:02:58,013] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 23:02:58,014] [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	83.9844	361	571	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_001487165.1	s__Blautia_A massiliensis	83.7051	340	571	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_003461955.1	s__Blautia_A sp900066335	83.5405	341	571	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_003474435.1	s__Blautia_A sp003474435	83.5353	347	571	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_013304825.1	s__Blautia_A schinkii	83.4496	352	571	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_900751995.1	s__Blautia_A sp900751995	82.873	238	571	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	95.05	95.05	0.55	0.55	2	-
GCA_900764225.1	s__Blautia_A sp900764225	82.0191	276	571	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	-
--------------------------------------------------------------------------------
[2023-06-05 23:02:58,015] [INFO] GTDB search result was written to GCA_934403785.1_ERR7745545_bin.146_genomic.fna/result_gtdb.tsv
[2023-06-05 23:02:58,016] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:02:58,018] [INFO] DFAST_QC result json was written to GCA_934403785.1_ERR7745545_bin.146_genomic.fna/dqc_result.json
[2023-06-05 23:02:58,019] [INFO] DFAST_QC completed!
[2023-06-05 23:02:58,019] [INFO] Total running time: 0h0m37s