[2023-06-13 03:40:46,602] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:40:46,612] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:40:46,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference
[2023-06-13 03:40:48,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:40:48,944] [INFO] Task started: Prodigal
[2023-06-13 03:40:48,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bbe4111-6c26-4463-b484-4ae2a97d773f/GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:40:58,308] [INFO] Task succeeded: Prodigal
[2023-06-13 03:40:58,309] [INFO] Task started: HMMsearch
[2023-06-13 03:40:58,309] [INFO] Running command: hmmsearch --tblout GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference/reference_markers.hmm GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:40:58,572] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:40:58,573] [INFO] Found 6/6 markers.
[2023-06-13 03:40:58,638] [INFO] Query marker FASTA was written to GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 03:40:58,638] [INFO] Task started: Blastn
[2023-06-13 03:40:58,638] [INFO] Running command: blastn -query GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference/reference_markers.fasta -out GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:40:59,277] [INFO] Task succeeded: Blastn
[2023-06-13 03:40:59,282] [INFO] Selected 27 target genomes.
[2023-06-13 03:40:59,283] [INFO] Target genome list was writen to GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 03:40:59,286] [INFO] Task started: fastANI
[2023-06-13 03:40:59,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bbe4111-6c26-4463-b484-4ae2a97d773f/GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:41:19,475] [INFO] Task succeeded: fastANI
[2023-06-13 03:41:19,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:41:19,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:41:19,491] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:41:19,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 03:41:19,492] [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
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.3791	103	1253	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.7519	65	1253	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6153	84	1253	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.5614	69	1253	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.5017	65	1253	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.481	64	1253	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.462	66	1253	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.3297	65	1253	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.307	73	1253	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.3049	71	1253	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.294	68	1253	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.2717	73	1253	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.2202	51	1253	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.1974	61	1253	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.1625	66	1253	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.1469	58	1253	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.144	68	1253	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	75.9546	58	1253	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	75.9542	65	1253	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	75.7787	63	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:41:19,494] [INFO] DFAST Taxonomy check result was written to GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 03:41:19,495] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:41:19,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:41:19,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference/checkm_data
[2023-06-13 03:41:19,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:41:19,581] [INFO] Task started: CheckM
[2023-06-13 03:41:19,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 03:41:51,587] [INFO] Task succeeded: CheckM
[2023-06-13 03:41:51,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:41:51,616] [INFO] ===== Completeness check finished =====
[2023-06-13 03:41:51,617] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:41:51,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 03:41:51,618] [INFO] Task started: Blastn
[2023-06-13 03:41:51,618] [INFO] Running command: blastn -query GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg526f44df-5f6a-40a8-95d4-bfd43fa7a8f3/dqc_reference/reference_markers_gtdb.fasta -out GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:41:52,707] [INFO] Task succeeded: Blastn
[2023-06-13 03:41:52,711] [INFO] Selected 8 target genomes.
[2023-06-13 03:41:52,711] [INFO] Target genome list was writen to GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:41:52,715] [INFO] Task started: fastANI
[2023-06-13 03:41:52,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bbe4111-6c26-4463-b484-4ae2a97d773f/GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:42:00,488] [INFO] Task succeeded: fastANI
[2023-06-13 03:42:00,500] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:42:00,500] [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_910575725.1	s__Merdisoma sp011959465	98.8594	1129	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.24	98.50	0.89	0.80	3	conclusive
GCA_910576325.1	s__Merdisoma sp910576325	84.3778	760	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	100.00	99.99	1.00	1.00	6	-
GCA_910574835.1	s__Merdisoma sp910574835	84.0164	747	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009917555.1	s__Merdisoma sp009917555	82.4149	704	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.22	99.22	0.93	0.93	2	-
GCA_910574255.1	s__Merdisoma sp910574255	81.6809	687	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.74	98.74	0.82	0.82	2	-
GCA_910586955.1	s__Merdisoma sp910586955	78.6465	347	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018376135.1	s__Choladocola sp018376135	76.8633	95	1253	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:42:00,502] [INFO] GTDB search result was written to GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 03:42:00,503] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:42:00,507] [INFO] DFAST_QC result json was written to GCA_947644775.1_SRR17794294_bin.70_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 03:42:00,507] [INFO] DFAST_QC completed!
[2023-06-13 03:42:00,507] [INFO] Total running time: 0h1m14s