[2023-06-30 14:48:11,108] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:48:11,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:48:11,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference
[2023-06-30 14:48:12,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:48:12,387] [INFO] Task started: Prodigal
[2023-06-30 14:48:12,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb49569-ad16-45dd-a393-59d0e488badd/GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:48:16,410] [INFO] Task succeeded: Prodigal
[2023-06-30 14:48:16,410] [INFO] Task started: HMMsearch
[2023-06-30 14:48:16,410] [INFO] Running command: hmmsearch --tblout GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference/reference_markers.hmm GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:48:16,625] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:48:16,626] [INFO] Found 6/6 markers.
[2023-06-30 14:48:16,648] [INFO] Query marker FASTA was written to GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-30 14:48:16,648] [INFO] Task started: Blastn
[2023-06-30 14:48:16,648] [INFO] Running command: blastn -query GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference/reference_markers.fasta -out GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:17,295] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:17,300] [INFO] Selected 33 target genomes.
[2023-06-30 14:48:17,301] [INFO] Target genome list was writen to GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-30 14:48:17,306] [INFO] Task started: fastANI
[2023-06-30 14:48:17,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb49569-ad16-45dd-a393-59d0e488badd/GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:48:35,656] [INFO] Task succeeded: fastANI
[2023-06-30 14:48:35,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:48:35,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:48:35,665] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:48:35,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:48:35,666] [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
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	75.311	51	453	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	75.1816	72	453	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.009	59	453	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	74.9403	55	453	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	74.9085	51	453	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.713	113	453	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.7094	114	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:48:35,668] [INFO] DFAST Taxonomy check result was written to GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-30 14:48:35,669] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:48:35,670] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:48:35,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference/checkm_data
[2023-06-30 14:48:35,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:48:35,704] [INFO] Task started: CheckM
[2023-06-30 14:48:35,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-30 14:48:54,716] [INFO] Task succeeded: CheckM
[2023-06-30 14:48:54,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:48:54,738] [INFO] ===== Completeness check finished =====
[2023-06-30 14:48:54,738] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:48:54,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-30 14:48:54,739] [INFO] Task started: Blastn
[2023-06-30 14:48:54,739] [INFO] Running command: blastn -query GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg51fc25a5-5315-448c-89a1-fdea7c3c5636/dqc_reference/reference_markers_gtdb.fasta -out GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:55,664] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:55,668] [INFO] Selected 21 target genomes.
[2023-06-30 14:48:55,668] [INFO] Target genome list was writen to GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:48:55,678] [INFO] Task started: fastANI
[2023-06-30 14:48:55,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb49569-ad16-45dd-a393-59d0e488badd/GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:49:04,754] [INFO] Task succeeded: fastANI
[2023-06-30 14:49:04,767] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:49:04,768] [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_018713405.1	s__Spyradenecus faecavium	99.1928	368	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__Spyradenecus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900771325.1	s__Spyradenecus sp900771325	80.8259	246	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__Spyradenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555175.1	s__Spyradenecus sp004555175	80.0948	223	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__Spyradenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558005.1	s__Spyradenecus sp017558005	77.4151	58	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__Spyradenecus	95.0	95.80	95.80	0.85	0.85	3	-
GCA_902770045.1	s__UBA1067 sp902770045	77.2261	86	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	95.51	95.51	0.70	0.70	2	-
GCA_902764415.1	s__UBA1067 sp002351765	77.187	87	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	97.23	96.23	0.86	0.81	5	-
GCA_017962605.1	s__RGIG5952 sp017962605	76.9355	75	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__JAAYLN01;g__RGIG5952	95.0	95.07	95.07	0.68	0.68	2	-
GCA_900547945.1	s__RUG572 sp900547945	76.7183	96	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	99.14	98.30	0.90	0.80	3	-
GCA_002449695.1	s__UBA1067 sp002449695	76.5301	69	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521875.1	s__JAAYLN01 sp012521875	76.4969	72	453	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__JAAYLN01;g__JAAYLN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:49:04,770] [INFO] GTDB search result was written to GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 14:49:04,770] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:49:04,774] [INFO] DFAST_QC result json was written to GCA_939799165.1_SRR2134645_bin.57_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-30 14:49:04,774] [INFO] DFAST_QC completed!
[2023-06-30 14:49:04,774] [INFO] Total running time: 0h0m54s