[2023-07-01 06:37:37,375] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:37:37,440] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:37:37,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference
[2023-07-01 06:37:38,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:37:38,749] [INFO] Task started: Prodigal
[2023-07-01 06:37:38,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg29f0840b-5d6f-4604-a062-7ef24b05b9a0/GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna.gz | prodigal -d GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/cds.fna -a GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:37:42,632] [INFO] Task succeeded: Prodigal
[2023-07-01 06:37:42,632] [INFO] Task started: HMMsearch
[2023-07-01 06:37:42,633] [INFO] Running command: hmmsearch --tblout GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference/reference_markers.hmm GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:37:42,855] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:37:42,857] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg29f0840b-5d6f-4604-a062-7ef24b05b9a0/GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna.gz]
[2023-07-01 06:37:42,877] [INFO] Query marker FASTA was written to GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/markers.fasta
[2023-07-01 06:37:42,877] [INFO] Task started: Blastn
[2023-07-01 06:37:42,878] [INFO] Running command: blastn -query GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference/reference_markers.fasta -out GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:37:43,695] [INFO] Task succeeded: Blastn
[2023-07-01 06:37:43,699] [INFO] Selected 11 target genomes.
[2023-07-01 06:37:43,700] [INFO] Target genome list was writen to GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/target_genomes.txt
[2023-07-01 06:37:43,702] [INFO] Task started: fastANI
[2023-07-01 06:37:43,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg29f0840b-5d6f-4604-a062-7ef24b05b9a0/GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna.gz --refList GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/target_genomes.txt --output GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:37:50,736] [INFO] Task succeeded: fastANI
[2023-07-01 06:37:50,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:37:50,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:37:50,744] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2023-07-01 06:37:50,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-07-01 06:37:50,745] [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
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	98.6206	357	373	95	conclusive
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	98.515	363	373	95	conclusive
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	98.4156	360	373	95	conclusive
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.3802	116	373	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.3302	120	373	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.1801	77	373	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.4826	52	373	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:37:50,747] [INFO] DFAST Taxonomy check result was written to GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/tc_result.tsv
[2023-07-01 06:37:50,748] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:37:50,748] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:37:50,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference/checkm_data
[2023-07-01 06:37:50,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:37:50,773] [INFO] Task started: CheckM
[2023-07-01 06:37:50,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/checkm_input GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/checkm_result
[2023-07-01 06:38:10,433] [INFO] Task succeeded: CheckM
[2023-07-01 06:38:10,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:38:10,454] [INFO] ===== Completeness check finished =====
[2023-07-01 06:38:10,454] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:38:10,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/markers.fasta)
[2023-07-01 06:38:10,455] [INFO] Task started: Blastn
[2023-07-01 06:38:10,455] [INFO] Running command: blastn -query GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4876bfe9-7801-463d-962a-c73ff4f3160a/dqc_reference/reference_markers_gtdb.fasta -out GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:38:11,251] [INFO] Task succeeded: Blastn
[2023-07-01 06:38:11,255] [INFO] Selected 9 target genomes.
[2023-07-01 06:38:11,255] [INFO] Target genome list was writen to GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:38:11,257] [INFO] Task started: fastANI
[2023-07-01 06:38:11,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg29f0840b-5d6f-4604-a062-7ef24b05b9a0/GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna.gz --refList GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:38:16,945] [INFO] Task succeeded: fastANI
[2023-07-01 06:38:16,959] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 06:38:16,959] [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_900537995.1	s__Roseburia intestinalis	98.515	363	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	conclusive
GCA_003483745.1	s__Roseburia sp003483745	90.8836	304	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCF_003470905.1	s__Roseburia sp003470905	90.7119	341	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_900550935.1	s__Roseburia sp900550935	78.9095	142	373	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_000174195.1	s__Roseburia inulinivorans	78.3603	116	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCA_900542495.1	s__Roseburia sp900542495	78.0998	114	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.47	97.09	0.82	0.76	4	-
GCA_902363825.1	s__CAG-45 sp000438375	77.9659	74	373	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_000225345.1	s__Roseburia hominis	77.3577	118	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCA_017937095.1	s__Roseburia sp017937095	77.1512	93	373	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:38:16,961] [INFO] GTDB search result was written to GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/result_gtdb.tsv
[2023-07-01 06:38:16,962] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:38:16,965] [INFO] DFAST_QC result json was written to GCA_943913385.1_hvLq8AUo3h_bin.46.MAG_genomic.fna/dqc_result.json
[2023-07-01 06:38:16,966] [INFO] DFAST_QC completed!
[2023-07-01 06:38:16,966] [INFO] Total running time: 0h0m40s