[2024-01-24 13:01:19,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference
[2024-01-24 13:01:20,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,765] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg62a3c0ec-e976-425f-869f-bd57ca2bcaa8/GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/cds.fna -a GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:33,837] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:33,838] [INFO] Task started: HMMsearch
[2024-01-24 13:01:33,838] [INFO] Running command: hmmsearch --tblout GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference/reference_markers.hmm GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:34,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:34,141] [INFO] Found 6/6 markers.
[2024-01-24 13:01:34,187] [INFO] Query marker FASTA was written to GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:34,187] [INFO] Task started: Blastn
[2024-01-24 13:01:34,187] [INFO] Running command: blastn -query GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference/reference_markers.fasta -out GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,762] [INFO] Selected 18 target genomes.
[2024-01-24 13:01:34,763] [INFO] Target genome list was writen to GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,785] [INFO] Task started: fastANI
[2024-01-24 13:01:34,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg62a3c0ec-e976-425f-869f-bd57ca2bcaa8/GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna.gz --refList GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:47,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:47,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:47,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:47,133] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:47,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:47,133] [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
Desulforhopalus singaporensis	strain=DSM 12130	GCA_900104445.1	91360	91360	type	True	100.0	1599	1605	95	conclusive
Desulfomarina profundi	strain=KT2	GCA_019703855.1	2772557	2772557	type	True	76.6295	76	1605	95	below_threshold
Desulfosediminicola flagellatus	strain=IMCC35005	GCA_005116655.2	2569541	2569541	type	True	76.6184	56	1605	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.1316	97	1605	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.1167	98	1605	95	below_threshold
Desulfofustis glycolicus	strain=DSM 9705	GCA_900130015.1	51195	51195	type	True	75.7799	74	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:47,134] [INFO] DFAST Taxonomy check result was written to GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:47,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:47,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:47,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference/checkm_data
[2024-01-24 13:01:47,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:47,188] [INFO] Task started: CheckM
[2024-01-24 13:01:47,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/checkm_input GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:28,619] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:28,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:28,642] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:28,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:28,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:28,644] [INFO] Task started: Blastn
[2024-01-24 13:02:28,644] [INFO] Running command: blastn -query GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3472b4da-6b92-4a4b-8a61-07eec65c11ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:29,361] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:29,366] [INFO] Selected 25 target genomes.
[2024-01-24 13:02:29,366] [INFO] Target genome list was writen to GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:29,393] [INFO] Task started: fastANI
[2024-01-24 13:02:29,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg62a3c0ec-e976-425f-869f-bd57ca2bcaa8/GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna.gz --refList GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:44,591] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:44,602] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:44,602] [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_900104445.1	s__Desulforhopalus singaporensis	100.0	1599	1605	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000961725.1	s__Desulforhopalus sp000961725	76.5872	155	1605	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919005.1	s__Desulfopila_A inferna	76.4983	67	1605	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila_A	95.0	95.27	95.27	0.87	0.87	2	-
GCA_001799365.1	s__Desulforhopalus sp001799365	76.3787	137	1605	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000769715.1	s__Desulfoprunum sp000769715	76.0549	93	1605	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.79	99.74	0.93	0.93	5	-
GCF_900130015.1	s__Desulfofustis glycolicus	75.7648	75	1605	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfofustis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,605] [INFO] GTDB search result was written to GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:44,605] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:44,608] [INFO] DFAST_QC result json was written to GCF_900104445.1_IMG-taxon_2596583525_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:44,608] [INFO] DFAST_QC completed!
[2024-01-24 13:02:44,608] [INFO] Total running time: 0h1m25s