[2023-06-05 08:42:11,624] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:42:11,629] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:42:11,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference
[2023-06-05 08:42:13,225] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:42:13,226] [INFO] Task started: Prodigal
[2023-06-05 08:42:13,226] [INFO] Running command: gunzip -c /var/lib/cwl/stgb827ad87-c4df-4d4a-aa01-556933e7ffad/GCA_934856015.1_MTG234_bin.42.fa_genomic.fna.gz | prodigal -d GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/cds.fna -a GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:42:15,484] [INFO] Task succeeded: Prodigal
[2023-06-05 08:42:15,485] [INFO] Task started: HMMsearch
[2023-06-05 08:42:15,485] [INFO] Running command: hmmsearch --tblout GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference/reference_markers.hmm GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:42:15,687] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:42:15,688] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb827ad87-c4df-4d4a-aa01-556933e7ffad/GCA_934856015.1_MTG234_bin.42.fa_genomic.fna.gz]
[2023-06-05 08:42:15,710] [INFO] Query marker FASTA was written to GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/markers.fasta
[2023-06-05 08:42:15,710] [INFO] Task started: Blastn
[2023-06-05 08:42:15,710] [INFO] Running command: blastn -query GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference/reference_markers.fasta -out GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:42:16,558] [INFO] Task succeeded: Blastn
[2023-06-05 08:42:16,563] [INFO] Selected 23 target genomes.
[2023-06-05 08:42:16,564] [INFO] Target genome list was writen to GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/target_genomes.txt
[2023-06-05 08:42:16,580] [INFO] Task started: fastANI
[2023-06-05 08:42:16,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgb827ad87-c4df-4d4a-aa01-556933e7ffad/GCA_934856015.1_MTG234_bin.42.fa_genomic.fna.gz --refList GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/target_genomes.txt --output GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:42:29,229] [INFO] Task succeeded: fastANI
[2023-06-05 08:42:29,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:42:29,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:42:29,240] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:42:29,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:42:29,240] [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
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	74.9238	51	464	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	74.9043	51	464	95	below_threshold
Clostridium combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	74.8827	61	464	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	74.8769	56	464	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	74.6776	59	464	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	74.6749	61	464	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	74.6659	62	464	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	74.6509	58	464	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:42:29,243] [INFO] DFAST Taxonomy check result was written to GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/tc_result.tsv
[2023-06-05 08:42:29,243] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:42:29,243] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:42:29,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference/checkm_data
[2023-06-05 08:42:29,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:42:29,267] [INFO] Task started: CheckM
[2023-06-05 08:42:29,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/checkm_input GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/checkm_result
[2023-06-05 08:42:44,544] [INFO] Task succeeded: CheckM
[2023-06-05 08:42:44,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:42:44,566] [INFO] ===== Completeness check finished =====
[2023-06-05 08:42:44,567] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:42:44,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/markers.fasta)
[2023-06-05 08:42:44,568] [INFO] Task started: Blastn
[2023-06-05 08:42:44,568] [INFO] Running command: blastn -query GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg938a63ee-b9f2-4584-8ead-38eb42573264/dqc_reference/reference_markers_gtdb.fasta -out GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:42:45,332] [INFO] Task succeeded: Blastn
[2023-06-05 08:42:45,336] [INFO] Selected 17 target genomes.
[2023-06-05 08:42:45,336] [INFO] Target genome list was writen to GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:42:45,343] [INFO] Task started: fastANI
[2023-06-05 08:42:45,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgb827ad87-c4df-4d4a-aa01-556933e7ffad/GCA_934856015.1_MTG234_bin.42.fa_genomic.fna.gz --refList GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:42:51,233] [INFO] Task succeeded: fastANI
[2023-06-05 08:42:51,246] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:42:51,246] [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_000438355.1	s__CAG-273 sp000438355	98.5313	367	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.50	98.37	0.86	0.79	3	conclusive
GCA_905215615.1	s__CAG-273 sp905215615	83.7687	208	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886645.1	s__CAG-273 sp017886645	81.106	265	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003507395.1	s__CAG-273 sp003507395	78.2143	152	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	99.04	98.89	0.89	0.87	5	-
GCA_900752095.1	s__CAG-273 sp900752095	77.6712	147	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	99.19	99.19	0.68	0.68	2	-
GCA_003534295.1	s__CAG-273 sp003534295	77.6588	143	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.76	98.52	0.84	0.83	5	-
GCA_000434015.1	s__CAG-492 sp000434015	77.6386	170	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.68	99.35	0.94	0.91	3	-
GCA_904381285.1	s__RGIG8482 sp904381285	77.5751	152	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__RGIG8482	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589185.1	s__CAG-273 sp910589185	77.524	133	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557195.1	s__CAG-492 sp900557195	77.5078	171	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554365.1	s__CAG-269 sp900554365	77.2392	130	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000437215.1	s__CAG-269 sp000437215	77.1954	147	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
GCA_017528375.1	s__CAG-492 sp017528375	77.0395	94	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430135.1	s__CAG-269 sp017430135	77.0095	126	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006345.1	s__Clostridium puniceum	74.6814	57	464	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:42:51,249] [INFO] GTDB search result was written to GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 08:42:51,250] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:42:51,255] [INFO] DFAST_QC result json was written to GCA_934856015.1_MTG234_bin.42.fa_genomic.fna/dqc_result.json
[2023-06-05 08:42:51,255] [INFO] DFAST_QC completed!
[2023-06-05 08:42:51,255] [INFO] Total running time: 0h0m40s