[2024-01-24 12:36:57,876] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:57,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:57,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference
[2024-01-24 12:36:59,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,262] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b4f6061-c20d-476b-8138-f188c55a6d1f/GCF_002933875.1_ASM293387v1_genomic.fna.gz | prodigal -d GCF_002933875.1_ASM293387v1_genomic.fna/cds.fna -a GCF_002933875.1_ASM293387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:08,826] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:08,827] [INFO] Task started: HMMsearch
[2024-01-24 12:37:08,827] [INFO] Running command: hmmsearch --tblout GCF_002933875.1_ASM293387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference/reference_markers.hmm GCF_002933875.1_ASM293387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:09,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:09,172] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4b4f6061-c20d-476b-8138-f188c55a6d1f/GCF_002933875.1_ASM293387v1_genomic.fna.gz]
[2024-01-24 12:37:09,206] [INFO] Query marker FASTA was written to GCF_002933875.1_ASM293387v1_genomic.fna/markers.fasta
[2024-01-24 12:37:09,207] [INFO] Task started: Blastn
[2024-01-24 12:37:09,207] [INFO] Running command: blastn -query GCF_002933875.1_ASM293387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference/reference_markers.fasta -out GCF_002933875.1_ASM293387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:09,833] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:09,836] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:09,837] [INFO] Target genome list was writen to GCF_002933875.1_ASM293387v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:09,859] [INFO] Task started: fastANI
[2024-01-24 12:37:09,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b4f6061-c20d-476b-8138-f188c55a6d1f/GCF_002933875.1_ASM293387v1_genomic.fna.gz --refList GCF_002933875.1_ASM293387v1_genomic.fna/target_genomes.txt --output GCF_002933875.1_ASM293387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:20,736] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:20,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:20,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:20,744] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:20,744] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:20,744] [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
Desulfocucumis palustris	strain=NAW-5	GCA_002933875.1	1898651	1898651	type	True	100.0	1164	1166	95	conclusive
Desulfurispora thermophila	strain=DSM 16022	GCA_000376385.1	265470	265470	type	True	76.8522	66	1166	95	below_threshold
Desulfofundulus thermosubterraneus	strain=DSM 16057	GCA_900142025.1	348840	348840	type	True	76.1208	55	1166	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:20,747] [INFO] DFAST Taxonomy check result was written to GCF_002933875.1_ASM293387v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:20,747] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:20,747] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:20,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference/checkm_data
[2024-01-24 12:37:20,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:20,790] [INFO] Task started: CheckM
[2024-01-24 12:37:20,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002933875.1_ASM293387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002933875.1_ASM293387v1_genomic.fna/checkm_input GCF_002933875.1_ASM293387v1_genomic.fna/checkm_result
[2024-01-24 12:37:53,440] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:53,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:53,466] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:53,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:53,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002933875.1_ASM293387v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:53,467] [INFO] Task started: Blastn
[2024-01-24 12:37:53,467] [INFO] Running command: blastn -query GCF_002933875.1_ASM293387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8524d4c1-a1a9-44af-9ce7-09f073f82842/dqc_reference/reference_markers_gtdb.fasta -out GCF_002933875.1_ASM293387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:54,293] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:54,297] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:54,297] [INFO] Target genome list was writen to GCF_002933875.1_ASM293387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:54,310] [INFO] Task started: fastANI
[2024-01-24 12:37:54,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b4f6061-c20d-476b-8138-f188c55a6d1f/GCF_002933875.1_ASM293387v1_genomic.fna.gz --refList GCF_002933875.1_ASM293387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002933875.1_ASM293387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:03,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,075] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:03,075] [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_002933875.1	s__Desulfocucumis palustris	100.0	1164	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfocucumaceae;g__Desulfocucumis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000233715.2	s__Sporotomaculum gibsoniae	78.9267	89	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfallaceae;g__Sporotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961595.1	s__Desulfocucumis sp000961595	78.8454	301	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfocucumaceae;g__Desulfocucumis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961585.1	s__BRHc4a sp000961585	77.4493	91	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfocucumaceae;g__BRHc4a	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000802095.1	s__BRHc4a sp000802095	77.0345	159	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfocucumaceae;g__BRHc4a	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000376385.1	s__Desulfurispora thermophila	76.8522	66	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfurisporaceae;g__Desulfurispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009428905.1	s__Desulfofundulus_A thermobenzoicus	76.2738	88	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus_A	95.0	96.96	95.37	0.88	0.86	3	-
GCF_900142025.1	s__Desulfofundulus thermosubterraneus	76.1208	55	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000214705.1	s__Desulfofundulus kuznetsovii	76.0907	61	1166	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfovirgulaceae;g__Desulfofundulus	95.0	97.21	97.21	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,077] [INFO] GTDB search result was written to GCF_002933875.1_ASM293387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:03,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:03,080] [INFO] DFAST_QC result json was written to GCF_002933875.1_ASM293387v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:03,080] [INFO] DFAST_QC completed!
[2024-01-24 12:38:03,080] [INFO] Total running time: 0h1m5s