[2023-06-05 02:34:36,020] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:34:36,022] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:34:36,023] [INFO] DQC Reference Directory: /var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference
[2023-06-05 02:34:37,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:34:37,313] [INFO] Task started: Prodigal
[2023-06-05 02:34:37,313] [INFO] Running command: gunzip -c /var/lib/cwl/stg96754511-dffa-4f48-b69d-9ea8b04f6e04/GCA_934415815.1_ERR7745438_bin.7_genomic.fna.gz | prodigal -d GCA_934415815.1_ERR7745438_bin.7_genomic.fna/cds.fna -a GCA_934415815.1_ERR7745438_bin.7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:34:44,930] [INFO] Task succeeded: Prodigal
[2023-06-05 02:34:44,930] [INFO] Task started: HMMsearch
[2023-06-05 02:34:44,930] [INFO] Running command: hmmsearch --tblout GCA_934415815.1_ERR7745438_bin.7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference/reference_markers.hmm GCA_934415815.1_ERR7745438_bin.7_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:34:45,214] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:34:45,215] [INFO] Found 6/6 markers.
[2023-06-05 02:34:45,245] [INFO] Query marker FASTA was written to GCA_934415815.1_ERR7745438_bin.7_genomic.fna/markers.fasta
[2023-06-05 02:34:45,245] [INFO] Task started: Blastn
[2023-06-05 02:34:45,245] [INFO] Running command: blastn -query GCA_934415815.1_ERR7745438_bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference/reference_markers.fasta -out GCA_934415815.1_ERR7745438_bin.7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:34:45,898] [INFO] Task succeeded: Blastn
[2023-06-05 02:34:45,903] [INFO] Selected 23 target genomes.
[2023-06-05 02:34:45,904] [INFO] Target genome list was writen to GCA_934415815.1_ERR7745438_bin.7_genomic.fna/target_genomes.txt
[2023-06-05 02:34:45,907] [INFO] Task started: fastANI
[2023-06-05 02:34:45,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg96754511-dffa-4f48-b69d-9ea8b04f6e04/GCA_934415815.1_ERR7745438_bin.7_genomic.fna.gz --refList GCA_934415815.1_ERR7745438_bin.7_genomic.fna/target_genomes.txt --output GCA_934415815.1_ERR7745438_bin.7_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:34:59,028] [INFO] Task succeeded: fastANI
[2023-06-05 02:34:59,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:34:59,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:34:59,047] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:34:59,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:34:59,047] [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 caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.3728	75	978	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.7615	113	978	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.7492	114	978	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.104	126	978	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.0815	128	978	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.0784	108	978	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	77.0653	123	978	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.023	59	978	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	76.9699	79	978	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.8944	95	978	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.8883	78	978	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.7412	56	978	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	76.4672	56	978	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.4562	61	978	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.239	62	978	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:34:59,050] [INFO] DFAST Taxonomy check result was written to GCA_934415815.1_ERR7745438_bin.7_genomic.fna/tc_result.tsv
[2023-06-05 02:34:59,050] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:34:59,050] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:34:59,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference/checkm_data
[2023-06-05 02:34:59,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:34:59,088] [INFO] Task started: CheckM
[2023-06-05 02:34:59,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934415815.1_ERR7745438_bin.7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934415815.1_ERR7745438_bin.7_genomic.fna/checkm_input GCA_934415815.1_ERR7745438_bin.7_genomic.fna/checkm_result
[2023-06-05 02:35:27,719] [INFO] Task succeeded: CheckM
[2023-06-05 02:35:27,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:35:27,745] [INFO] ===== Completeness check finished =====
[2023-06-05 02:35:27,745] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:35:27,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934415815.1_ERR7745438_bin.7_genomic.fna/markers.fasta)
[2023-06-05 02:35:27,746] [INFO] Task started: Blastn
[2023-06-05 02:35:27,746] [INFO] Running command: blastn -query GCA_934415815.1_ERR7745438_bin.7_genomic.fna/markers.fasta -db /var/lib/cwl/stg51f7d593-cfc2-4801-a631-bad5826ce116/dqc_reference/reference_markers_gtdb.fasta -out GCA_934415815.1_ERR7745438_bin.7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:35:28,791] [INFO] Task succeeded: Blastn
[2023-06-05 02:35:28,796] [INFO] Selected 19 target genomes.
[2023-06-05 02:35:28,796] [INFO] Target genome list was writen to GCA_934415815.1_ERR7745438_bin.7_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:35:28,809] [INFO] Task started: fastANI
[2023-06-05 02:35:28,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg96754511-dffa-4f48-b69d-9ea8b04f6e04/GCA_934415815.1_ERR7745438_bin.7_genomic.fna.gz --refList GCA_934415815.1_ERR7745438_bin.7_genomic.fna/target_genomes_gtdb.txt --output GCA_934415815.1_ERR7745438_bin.7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:35:40,572] [INFO] Task succeeded: fastANI
[2023-06-05 02:35:40,588] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:35:40,588] [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
GCA_902363135.1	s__Choladousia sp902363135	95.5398	826	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	conclusive
GCA_902363665.1	s__Choladousia sp902363665	79.731	381	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCA_002491565.1	s__Choladousia sp002491565	78.1781	220	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015557635.1	s__Fusicatenibacter saccharivorans	77.6781	121	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	97.82	97.27	0.86	0.77	91	-
GCA_018223435.1	s__Limivivens sp900543575	77.6318	120	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	-
GCA_003612585.1	s__Choladousia sp003612585	77.6003	145	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757145.1	s__Choladousia sp900757145	77.4715	120	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	99.16	99.16	0.96	0.96	2	-
GCA_004557975.1	s__Choladousia sp004557975	77.3238	193	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711885.1	s__Choladousia intestinipullorum	77.316	135	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000173815.1	s__Marvinbryantia formatexigens	77.0653	123	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.98	99.98	0.99	0.99	3	-
GCA_016297895.1	s__Marvinbryantia sp016297895	76.9945	77	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553635.1	s__Merdisoma sp900553635	76.9375	61	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	97.48	97.13	0.82	0.78	3	-
GCF_003470905.1	s__Roseburia sp003470905	76.8544	58	978	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_905207905.1	s__Merdiplasma sp905207905	76.8125	65	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696065.1	s__Oliverpabstia intestinalis	76.5772	77	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
GCA_018366495.1	s__JAGZHZ01 sp018366495	76.4816	56	978	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGZHZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:35:40,590] [INFO] GTDB search result was written to GCA_934415815.1_ERR7745438_bin.7_genomic.fna/result_gtdb.tsv
[2023-06-05 02:35:40,590] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:35:40,594] [INFO] DFAST_QC result json was written to GCA_934415815.1_ERR7745438_bin.7_genomic.fna/dqc_result.json
[2023-06-05 02:35:40,594] [INFO] DFAST_QC completed!
[2023-06-05 02:35:40,594] [INFO] Total running time: 0h1m5s