[2023-06-08 17:47:27,999] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:47:28,001] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:47:28,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference
[2023-06-08 17:47:29,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:47:29,275] [INFO] Task started: Prodigal
[2023-06-08 17:47:29,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgca102fd1-e937-42ec-8962-343a543cc3ca/GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:47:31,121] [INFO] Task succeeded: Prodigal
[2023-06-08 17:47:31,121] [INFO] Task started: HMMsearch
[2023-06-08 17:47:31,121] [INFO] Running command: hmmsearch --tblout GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference/reference_markers.hmm GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:47:31,338] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:47:31,339] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgca102fd1-e937-42ec-8962-343a543cc3ca/GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 17:47:31,359] [INFO] Query marker FASTA was written to GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 17:47:31,360] [INFO] Task started: Blastn
[2023-06-08 17:47:31,360] [INFO] Running command: blastn -query GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference/reference_markers.fasta -out GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:31,927] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:31,936] [INFO] Selected 25 target genomes.
[2023-06-08 17:47:31,936] [INFO] Target genome list was writen to GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:47:31,939] [INFO] Task started: fastANI
[2023-06-08 17:47:31,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgca102fd1-e937-42ec-8962-343a543cc3ca/GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:47:41,149] [INFO] Task succeeded: fastANI
[2023-06-08 17:47:41,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:47:41,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:47:41,157] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:47:41,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:47:41,157] [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
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	74.6183	53	436	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:47:41,160] [INFO] DFAST Taxonomy check result was written to GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:47:41,160] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:47:41,160] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:47:41,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference/checkm_data
[2023-06-08 17:47:41,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:47:41,185] [INFO] Task started: CheckM
[2023-06-08 17:47:41,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 17:47:55,349] [INFO] Task succeeded: CheckM
[2023-06-08 17:47:55,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:47:55,370] [INFO] ===== Completeness check finished =====
[2023-06-08 17:47:55,371] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:47:55,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:47:55,372] [INFO] Task started: Blastn
[2023-06-08 17:47:55,372] [INFO] Running command: blastn -query GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5091a047-03e6-4cc1-8838-64b5c15b9f9b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:56,153] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:56,157] [INFO] Selected 24 target genomes.
[2023-06-08 17:47:56,158] [INFO] Target genome list was writen to GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:47:56,166] [INFO] Task started: fastANI
[2023-06-08 17:47:56,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgca102fd1-e937-42ec-8962-343a543cc3ca/GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:01,172] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:01,191] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 17:48:01,192] [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_015059285.1	s__SIG208 sp015059285	81.1039	215	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461465.1	s__RGIG4266 sp017461465	77.9733	81	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550255.1	s__UBA5026 sp900550255	77.6824	91	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_015059195.1	s__SIG204 sp015059195	77.3742	61	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG204	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936845.1	s__UBA5026 sp017936845	77.3524	112	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432855.1	s__Coprosoma sp000432855	77.1201	55	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017887425.1	s__Faecisoma sp017887425	77.0874	88	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905206805.1	s__CAJLIR01 sp905206805	77.0467	109	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAJLIR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059365.1	s__SIG204 sp015059365	76.8932	85	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG204	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544605.1	s__SIG204 sp900544605	76.8871	116	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG204	95.0	98.54	98.50	0.89	0.86	3	-
GCA_017940575.1	s__UBA5026 sp017940575	76.8747	76	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801685.1	s__RUG12438 sp902801685	76.8706	60	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG12438	95.0	98.56	98.56	0.78	0.78	2	-
GCA_017527675.1	s__RGIG6635 sp017527675	76.8583	72	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG6635	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282155.1	s__RGIG4266 sp016282155	76.7901	77	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520435.1	s__JAAYOI01 sp012520435	76.7873	106	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546245.1	s__CAG-433 sp900546245	76.7088	66	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	97.58	97.10	0.81	0.77	4	-
GCA_017462455.1	s__UMGS1613 sp017462455	76.672	88	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428495.1	s__CAG-1193 sp017428495	75.7822	62	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	98.47	98.35	0.88	0.84	3	-
GCA_910587745.1	s__Caccenecus sp910587745	75.6262	56	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Caccenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211265.1	s__HGM10818 sp905211265	75.5239	64	436	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:01,193] [INFO] GTDB search result was written to GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:01,194] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:01,197] [INFO] DFAST_QC result json was written to GCA_947646095.1_SRR15730532_bin.52_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:48:01,198] [INFO] DFAST_QC completed!
[2023-06-08 17:48:01,198] [INFO] Total running time: 0h0m33s