[2023-06-05 10:23:52,198] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:23:52,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:23:52,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference
[2023-06-05 10:23:54,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:23:54,076] [INFO] Task started: Prodigal
[2023-06-05 10:23:54,077] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbe21efc-9eb1-4cb1-8733-b863c832e10a/GCA_934835005.1_MTG227_bin.10.fa_genomic.fna.gz | prodigal -d GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/cds.fna -a GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:23:59,957] [INFO] Task succeeded: Prodigal
[2023-06-05 10:23:59,957] [INFO] Task started: HMMsearch
[2023-06-05 10:23:59,957] [INFO] Running command: hmmsearch --tblout GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference/reference_markers.hmm GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:24:00,203] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:24:00,204] [INFO] Found 6/6 markers.
[2023-06-05 10:24:00,229] [INFO] Query marker FASTA was written to GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/markers.fasta
[2023-06-05 10:24:00,230] [INFO] Task started: Blastn
[2023-06-05 10:24:00,230] [INFO] Running command: blastn -query GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference/reference_markers.fasta -out GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:24:00,810] [INFO] Task succeeded: Blastn
[2023-06-05 10:24:00,815] [INFO] Selected 22 target genomes.
[2023-06-05 10:24:00,816] [INFO] Target genome list was writen to GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/target_genomes.txt
[2023-06-05 10:24:00,820] [INFO] Task started: fastANI
[2023-06-05 10:24:00,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe21efc-9eb1-4cb1-8733-b863c832e10a/GCA_934835005.1_MTG227_bin.10.fa_genomic.fna.gz --refList GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/target_genomes.txt --output GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:24:12,315] [INFO] Task succeeded: fastANI
[2023-06-05 10:24:12,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:24:12,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:24:12,333] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:24:12,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:24:12,333] [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_900537995.1	166486	166486	type	True	78.2673	158	841	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	78.2263	158	841	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	78.1886	163	841	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.7671	108	841	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.5852	135	841	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.5237	175	841	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	77.2588	81	841	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.0904	71	841	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.9472	79	841	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.8299	67	841	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	76.7977	84	841	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.6443	81	841	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.6102	81	841	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	76.4906	55	841	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	76.1034	60	841	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:24:12,335] [INFO] DFAST Taxonomy check result was written to GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/tc_result.tsv
[2023-06-05 10:24:12,336] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:24:12,336] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:24:12,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference/checkm_data
[2023-06-05 10:24:12,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:24:12,365] [INFO] Task started: CheckM
[2023-06-05 10:24:12,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/checkm_input GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/checkm_result
[2023-06-05 10:24:36,004] [INFO] Task succeeded: CheckM
[2023-06-05 10:24:36,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:24:36,026] [INFO] ===== Completeness check finished =====
[2023-06-05 10:24:36,027] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:24:36,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/markers.fasta)
[2023-06-05 10:24:36,027] [INFO] Task started: Blastn
[2023-06-05 10:24:36,028] [INFO] Running command: blastn -query GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg2de1f59b-9dff-4132-9492-6236f208bdd5/dqc_reference/reference_markers_gtdb.fasta -out GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:24:36,863] [INFO] Task succeeded: Blastn
[2023-06-05 10:24:36,871] [INFO] Selected 15 target genomes.
[2023-06-05 10:24:36,871] [INFO] Target genome list was writen to GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:24:36,878] [INFO] Task started: fastANI
[2023-06-05 10:24:36,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe21efc-9eb1-4cb1-8733-b863c832e10a/GCA_934835005.1_MTG227_bin.10.fa_genomic.fna.gz --refList GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:24:44,743] [INFO] Task succeeded: fastANI
[2023-06-05 10:24:44,769] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:24:44,769] [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_003479605.1	s__RUG115 sp900066395	97.7637	724	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	conclusive
GCA_900315735.1	s__RUG115 sp900315735	94.0857	677	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
GCF_014287635.1	s__1XD42-69 sp014287635	78.0908	176	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	-
GCA_902782995.1	s__RUG115 sp902782995	78.0805	186	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519695.1	s__14-2 sp012519695	77.9334	166	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	97.81	97.81	0.86	0.86	2	-
GCF_001940165.1	s__Roseburia sp001940165	77.8519	184	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470905.1	s__Roseburia sp003470905	77.8105	151	841	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_902363825.1	s__CAG-45 sp000438375	77.5067	138	841	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	-
GCA_003507655.1	s__UBA11774 sp003507655	77.4922	127	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11774	95.0	98.49	98.09	0.91	0.83	6	-
GCA_910578885.1	s__RUG115 sp910578885	77.459	150	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483745.1	s__Roseburia sp003483745	77.4203	168	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900550935.1	s__Roseburia sp900550935	77.0658	137	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_017484135.1	s__RUG115 sp017484135	76.8914	79	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548765.1	s__Agathobacter sp900548765	76.6439	77	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	97.03	0.78	0.78	2	-
GCA_905216215.1	s__Bariatricus sp905216215	75.8023	55	841	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:24:44,771] [INFO] GTDB search result was written to GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 10:24:44,772] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:24:44,776] [INFO] DFAST_QC result json was written to GCA_934835005.1_MTG227_bin.10.fa_genomic.fna/dqc_result.json
[2023-06-05 10:24:44,776] [INFO] DFAST_QC completed!
[2023-06-05 10:24:44,776] [INFO] Total running time: 0h0m53s