[2023-06-05 13:16:17,148] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:16:17,150] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:16:17,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference
[2023-06-05 13:16:18,481] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:16:18,482] [INFO] Task started: Prodigal
[2023-06-05 13:16:18,483] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdd694c3-27de-461a-89c6-cd5e9668caf1/GCA_934839265.1_MTG231_bin.18.fa_genomic.fna.gz | prodigal -d GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/cds.fna -a GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:16:23,430] [INFO] Task succeeded: Prodigal
[2023-06-05 13:16:23,431] [INFO] Task started: HMMsearch
[2023-06-05 13:16:23,431] [INFO] Running command: hmmsearch --tblout GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference/reference_markers.hmm GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:16:23,658] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:16:23,659] [INFO] Found 6/6 markers.
[2023-06-05 13:16:23,686] [INFO] Query marker FASTA was written to GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/markers.fasta
[2023-06-05 13:16:23,686] [INFO] Task started: Blastn
[2023-06-05 13:16:23,686] [INFO] Running command: blastn -query GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference/reference_markers.fasta -out GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:16:24,254] [INFO] Task succeeded: Blastn
[2023-06-05 13:16:24,258] [INFO] Selected 11 target genomes.
[2023-06-05 13:16:24,258] [INFO] Target genome list was writen to GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/target_genomes.txt
[2023-06-05 13:16:24,259] [INFO] Task started: fastANI
[2023-06-05 13:16:24,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd694c3-27de-461a-89c6-cd5e9668caf1/GCA_934839265.1_MTG231_bin.18.fa_genomic.fna.gz --refList GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/target_genomes.txt --output GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:16:31,132] [INFO] Task succeeded: fastANI
[2023-06-05 13:16:31,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:16:31,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:16:31,142] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2023-06-05 13:16:31,143] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 13:16:31,143] [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
Intestinibacter bartlettii	strain=DSM 16795	GCA_025148965.1	261299	261299	type	True	98.9748	905	1012	95	conclusive
Intestinibacter bartlettii	strain=DSM 16795	GCA_000154445.1	261299	261299	type	True	98.9456	900	1012	95	conclusive
Intestinibacter bartlettii	strain=DSM 16795	GCA_900167285.1	261299	261299	type	True	98.9033	903	1012	95	conclusive
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	78.7094	335	1012	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	78.4653	302	1012	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	78.3982	228	1012	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	78.123	269	1012	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	77.6291	269	1012	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	77.5462	218	1012	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	77.4739	228	1012	95	below_threshold
Clostridioides difficile	strain=ATCC 9689	GCA_000376285.1	1496	1496	type	True	77.218	217	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:16:31,145] [INFO] DFAST Taxonomy check result was written to GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/tc_result.tsv
[2023-06-05 13:16:31,145] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:16:31,146] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:16:31,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference/checkm_data
[2023-06-05 13:16:31,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:16:31,180] [INFO] Task started: CheckM
[2023-06-05 13:16:31,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/checkm_input GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/checkm_result
[2023-06-05 13:16:53,397] [INFO] Task succeeded: CheckM
[2023-06-05 13:16:53,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.28%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:16:53,421] [INFO] ===== Completeness check finished =====
[2023-06-05 13:16:53,422] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:16:53,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/markers.fasta)
[2023-06-05 13:16:53,423] [INFO] Task started: Blastn
[2023-06-05 13:16:53,423] [INFO] Running command: blastn -query GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg755c115f-40e8-40f3-8c1d-68d7c6ee1a6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:16:54,273] [INFO] Task succeeded: Blastn
[2023-06-05 13:16:54,277] [INFO] Selected 10 target genomes.
[2023-06-05 13:16:54,277] [INFO] Target genome list was writen to GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:16:54,282] [INFO] Task started: fastANI
[2023-06-05 13:16:54,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd694c3-27de-461a-89c6-cd5e9668caf1/GCA_934839265.1_MTG231_bin.18.fa_genomic.fna.gz --refList GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:17:00,777] [INFO] Task succeeded: fastANI
[2023-06-05 13:17:00,787] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:17:00,788] [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_000154445.1	s__Intestinibacter bartlettii	98.9497	899	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter	95.0	98.74	98.25	0.89	0.55	12	conclusive
GCF_018917435.1	s__Intestinibacter bartlettii_A	88.8591	781	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667935.1	s__Intestinibacter sp900540355	87.5746	656	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter	95.0	99.12	98.96	0.88	0.87	4	-
GCA_900557165.1	s__Terrisporobacter sp900557165	80.116	249	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
GCA_902363255.1	s__Terrisporobacter sp902363255	79.0516	326	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333445.1	s__Terrisporobacter mayombei	78.7528	194	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017888745.1	s__Terrisporobacter sp017888745	78.4628	288	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362365.1	s__GCA-900066495 sp902362365	78.3892	258	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323405.1	s__GCA-900066495 sp014323405	78.1799	257	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900604495.1	s__GCA-900066495 sp900066495	78.153	276	1012	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	99.74	99.60	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2023-06-05 13:17:00,790] [INFO] GTDB search result was written to GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 13:17:00,790] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:17:00,794] [INFO] DFAST_QC result json was written to GCA_934839265.1_MTG231_bin.18.fa_genomic.fna/dqc_result.json
[2023-06-05 13:17:00,795] [INFO] DFAST_QC completed!
[2023-06-05 13:17:00,795] [INFO] Total running time: 0h0m44s