[2024-01-24 14:31:14,285] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference
[2024-01-24 14:31:15,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,612] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg954999e8-4c10-48da-9874-5bbf931cdd59/GCF_005377625.1_ASM537762v1_genomic.fna.gz | prodigal -d GCF_005377625.1_ASM537762v1_genomic.fna/cds.fna -a GCF_005377625.1_ASM537762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:26,359] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:26,360] [INFO] Task started: HMMsearch
[2024-01-24 14:31:26,360] [INFO] Running command: hmmsearch --tblout GCF_005377625.1_ASM537762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference/reference_markers.hmm GCF_005377625.1_ASM537762v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:26,682] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:26,683] [INFO] Found 6/6 markers.
[2024-01-24 14:31:26,717] [INFO] Query marker FASTA was written to GCF_005377625.1_ASM537762v1_genomic.fna/markers.fasta
[2024-01-24 14:31:26,717] [INFO] Task started: Blastn
[2024-01-24 14:31:26,717] [INFO] Running command: blastn -query GCF_005377625.1_ASM537762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference/reference_markers.fasta -out GCF_005377625.1_ASM537762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:27,464] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:27,467] [INFO] Selected 20 target genomes.
[2024-01-24 14:31:27,468] [INFO] Target genome list was writen to GCF_005377625.1_ASM537762v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:27,475] [INFO] Task started: fastANI
[2024-01-24 14:31:27,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg954999e8-4c10-48da-9874-5bbf931cdd59/GCF_005377625.1_ASM537762v1_genomic.fna.gz --refList GCF_005377625.1_ASM537762v1_genomic.fna/target_genomes.txt --output GCF_005377625.1_ASM537762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:45,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:45,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:45,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:45,327] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:45,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:45,328] [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
Desulfoglaeba alkanexedens	strain=ALDC	GCA_005377625.1	361111	361111	type	True	100.0	1121	1121	95	conclusive
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	77.3749	247	1121	95	below_threshold
Desulfacinum hydrothermale	strain=DSM 13146	GCA_900176285.1	109258	109258	type	True	77.1511	199	1121	95	below_threshold
Syntrophobacter fumaroxidans	strain=MPOB	GCA_000014965.1	119484	119484	type	True	77.0229	84	1121	95	below_threshold
Desulfoferrobacter suflitae	strain=DRH4	GCA_022603395.1	2865782	2865782	type	True	76.8174	69	1121	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.7641	55	1121	95	below_threshold
Desulfosoma caldarium	strain=DSM 22027	GCA_003751385.1	610254	610254	type	True	76.6979	116	1121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:45,330] [INFO] DFAST Taxonomy check result was written to GCF_005377625.1_ASM537762v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:45,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:45,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:45,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference/checkm_data
[2024-01-24 14:31:45,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:45,367] [INFO] Task started: CheckM
[2024-01-24 14:31:45,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005377625.1_ASM537762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005377625.1_ASM537762v1_genomic.fna/checkm_input GCF_005377625.1_ASM537762v1_genomic.fna/checkm_result
[2024-01-24 14:32:20,342] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:20,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,371] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:20,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:20,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005377625.1_ASM537762v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:20,372] [INFO] Task started: Blastn
[2024-01-24 14:32:20,373] [INFO] Running command: blastn -query GCF_005377625.1_ASM537762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a878089-a7a2-41b8-af7d-a233ad7420c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_005377625.1_ASM537762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:21,284] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:21,288] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:21,288] [INFO] Target genome list was writen to GCF_005377625.1_ASM537762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:21,312] [INFO] Task started: fastANI
[2024-01-24 14:32:21,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg954999e8-4c10-48da-9874-5bbf931cdd59/GCF_005377625.1_ASM537762v1_genomic.fna.gz --refList GCF_005377625.1_ASM537762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005377625.1_ASM537762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:33,815] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:33,828] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:33,829] [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_005377625.1	s__Desulfoglaeba alkanexedens	100.0	1120	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfoglaeba	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014359885.1	s__Desulfacinum sp014359885	77.5378	253	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129305.1	s__Desulfacinum infernum	77.3758	247	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176285.1	s__Desulfacinum hydrothermale	77.1786	198	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014965.1	s__Syntrophobacter fumaroxidans	76.8472	83	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__Syntrophobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751385.1	s__Desulfosoma caldarium	76.7067	116	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011329395.1	s__Desulfosoma infernum_A	76.6937	185	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873705.1	s__CG2-30-61-12 sp001873705	76.6647	121	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__CG2-30-61-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011328915.1	s__DSUX01 sp011328915	76.4427	92	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__DSUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603845.1	s__SbD1 sp001603845	76.3889	79	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018053185.1	s__JAGPLX01 sp018053185	76.174	65	1121	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAGPLX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:33,831] [INFO] GTDB search result was written to GCF_005377625.1_ASM537762v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:33,832] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:33,837] [INFO] DFAST_QC result json was written to GCF_005377625.1_ASM537762v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:33,837] [INFO] DFAST_QC completed!
[2024-01-24 14:32:33,837] [INFO] Total running time: 0h1m20s