[2023-06-17 15:15:54,311] [INFO] DFAST_QC pipeline started.
[2023-06-17 15:15:54,314] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 15:15:54,314] [INFO] DQC Reference Directory: /var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference
[2023-06-17 15:15:55,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 15:15:55,607] [INFO] Task started: Prodigal
[2023-06-17 15:15:55,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg15967bd5-8fd2-4ff2-8e5b-039a540fc141/GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna.gz | prodigal -d GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/cds.fna -a GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 15:15:59,509] [INFO] Task succeeded: Prodigal
[2023-06-17 15:15:59,510] [INFO] Task started: HMMsearch
[2023-06-17 15:15:59,510] [INFO] Running command: hmmsearch --tblout GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference/reference_markers.hmm GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/protein.faa > /dev/null
[2023-06-17 15:15:59,707] [INFO] Task succeeded: HMMsearch
[2023-06-17 15:15:59,708] [INFO] Found 6/6 markers.
[2023-06-17 15:15:59,729] [INFO] Query marker FASTA was written to GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/markers.fasta
[2023-06-17 15:15:59,729] [INFO] Task started: Blastn
[2023-06-17 15:15:59,729] [INFO] Running command: blastn -query GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/markers.fasta -db /var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference/reference_markers.fasta -out GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:16:00,354] [INFO] Task succeeded: Blastn
[2023-06-17 15:16:00,360] [INFO] Selected 20 target genomes.
[2023-06-17 15:16:00,360] [INFO] Target genome list was writen to GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/target_genomes.txt
[2023-06-17 15:16:00,363] [INFO] Task started: fastANI
[2023-06-17 15:16:00,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg15967bd5-8fd2-4ff2-8e5b-039a540fc141/GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna.gz --refList GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/target_genomes.txt --output GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 15:16:09,645] [INFO] Task succeeded: fastANI
[2023-06-17 15:16:09,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 15:16:09,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 15:16:09,658] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 15:16:09,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 15:16:09,659] [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
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	84.3843	458	548	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	78.1289	145	548	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.9091	136	548	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.8172	136	548	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.813	119	548	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.7182	118	548	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.6921	120	548	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.6316	119	548	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	77.2769	122	548	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.2152	76	548	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	76.5823	81	548	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	76.4263	70	548	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	76.2756	57	548	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 15:16:09,662] [INFO] DFAST Taxonomy check result was written to GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/tc_result.tsv
[2023-06-17 15:16:09,663] [INFO] ===== Taxonomy check completed =====
[2023-06-17 15:16:09,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 15:16:09,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference/checkm_data
[2023-06-17 15:16:09,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 15:16:09,688] [INFO] Task started: CheckM
[2023-06-17 15:16:09,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/checkm_input GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/checkm_result
[2023-06-17 15:16:28,728] [INFO] Task succeeded: CheckM
[2023-06-17 15:16:28,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 15:16:28,747] [INFO] ===== Completeness check finished =====
[2023-06-17 15:16:28,748] [INFO] ===== Start GTDB Search =====
[2023-06-17 15:16:28,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/markers.fasta)
[2023-06-17 15:16:28,748] [INFO] Task started: Blastn
[2023-06-17 15:16:28,748] [INFO] Running command: blastn -query GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/markers.fasta -db /var/lib/cwl/stgda26b7bb-76c6-4393-bb8f-b19b95053416/dqc_reference/reference_markers_gtdb.fasta -out GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 15:16:29,798] [INFO] Task succeeded: Blastn
[2023-06-17 15:16:29,803] [INFO] Selected 19 target genomes.
[2023-06-17 15:16:29,803] [INFO] Target genome list was writen to GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 15:16:29,810] [INFO] Task started: fastANI
[2023-06-17 15:16:29,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg15967bd5-8fd2-4ff2-8e5b-039a540fc141/GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna.gz --refList GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/target_genomes_gtdb.txt --output GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 15:16:38,115] [INFO] Task succeeded: fastANI
[2023-06-17 15:16:38,130] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 15:16:38,130] [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_905209865.1	s__Mediterraneibacter sp900752395	100.0	540	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	conclusive
GCF_000153925.1	s__Mediterraneibacter torques	84.4005	457	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.42	99.19	0.88	0.82	25	-
GCA_900556835.1	s__Faecalimonas sp900556835	79.4882	78	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113645.1	s__Mediterraneibacter vanvlietii	78.4814	148	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	78.0127	112	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCF_000155205.1	s__Mediterraneibacter lactaris	77.9346	135	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_904377845.1	s__Mediterraneibacter sp904377845	77.884	152	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	77.7809	133	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_019119675.1	s__Mediterraneibacter faecipullorum	77.7736	131	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904418845.1	s__Mediterraneibacter sp904418845	77.7362	140	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	77.5821	129	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCA_001312505.1	s__Mediterraneibacter faecis	77.4282	125	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCA_019112735.1	s__Mediterraneibacter guildfordensis	77.3854	116	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115385.1	s__Mediterraneibacter avicola	77.3684	113	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.73	98.73	0.86	0.86	2	-
GCF_900120155.1	s__Mediterraneibacter sp900120155	77.3202	133	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112765.1	s__Mediterraneibacter norwichensis	77.2315	116	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.85	97.86	0.81	0.76	3	-
GCA_019117305.1	s__Mediterraneibacter merdigallinarum	76.7981	106	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 15:16:38,132] [INFO] GTDB search result was written to GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/result_gtdb.tsv
[2023-06-17 15:16:38,133] [INFO] ===== GTDB Search completed =====
[2023-06-17 15:16:38,137] [INFO] DFAST_QC result json was written to GCA_905209865.1_ERR260246-mag-bin.2_genomic.fna/dqc_result.json
[2023-06-17 15:16:38,138] [INFO] DFAST_QC completed!
[2023-06-17 15:16:38,138] [INFO] Total running time: 0h0m44s