[2024-01-24 13:17:46,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:46,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:46,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference
[2024-01-24 13:17:47,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:47,529] [INFO] Task started: Prodigal
[2024-01-24 13:17:47,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e43ea2c-cfc6-4f59-ba00-d5bfd50edaff/GCF_000189755.2_ASM18975v3_genomic.fna.gz | prodigal -d GCF_000189755.2_ASM18975v3_genomic.fna/cds.fna -a GCF_000189755.2_ASM18975v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:55,133] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:55,133] [INFO] Task started: HMMsearch
[2024-01-24 13:17:55,134] [INFO] Running command: hmmsearch --tblout GCF_000189755.2_ASM18975v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference/reference_markers.hmm GCF_000189755.2_ASM18975v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:55,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:55,427] [INFO] Found 6/6 markers.
[2024-01-24 13:17:55,456] [INFO] Query marker FASTA was written to GCF_000189755.2_ASM18975v3_genomic.fna/markers.fasta
[2024-01-24 13:17:55,456] [INFO] Task started: Blastn
[2024-01-24 13:17:55,456] [INFO] Running command: blastn -query GCF_000189755.2_ASM18975v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference/reference_markers.fasta -out GCF_000189755.2_ASM18975v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:56,071] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:56,075] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:56,075] [INFO] Target genome list was writen to GCF_000189755.2_ASM18975v3_genomic.fna/target_genomes.txt
[2024-01-24 13:17:56,081] [INFO] Task started: fastANI
[2024-01-24 13:17:56,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e43ea2c-cfc6-4f59-ba00-d5bfd50edaff/GCF_000189755.2_ASM18975v3_genomic.fna.gz --refList GCF_000189755.2_ASM18975v3_genomic.fna/target_genomes.txt --output GCF_000189755.2_ASM18975v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:03,142] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:03,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:03,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:03,151] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:03,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:03,152] [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
Desulfotomaculum nigrificans	strain=DSM 574	GCA_000189755.3	1565	1565	type	True	100.0	1017	1017	95	conclusive
Desulforamulus putei	strain=DSM 12395	GCA_900129195.1	74701	74701	type	True	80.6816	336	1017	95	below_threshold
Desulforamulus profundi	strain=Bs107	GCA_002607855.1	1383067	1383067	type	True	80.2086	300	1017	95	below_threshold
Desulforamulus hydrothermalis	strain=Lam5	GCA_000315365.1	412895	412895	type	True	79.6824	246	1017	95	below_threshold
Desulforamulus ferrireducens	strain=GSS09	GCA_002005145.1	1833852	1833852	type	True	79.5195	235	1017	95	below_threshold
Desulforamulus hydrothermalis	strain=DSM 18033	GCA_900129895.1	412895	412895	type	True	79.2083	239	1017	95	below_threshold
Desulforamulus reducens	strain=MI-1	GCA_000016165.1	59610	59610	type	True	78.9297	192	1017	95	below_threshold
Desulforamulus ruminis	strain=DSM 2154	GCA_000215085.1	1564	1564	type	True	78.1996	224	1017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:03,153] [INFO] DFAST Taxonomy check result was written to GCF_000189755.2_ASM18975v3_genomic.fna/tc_result.tsv
[2024-01-24 13:18:03,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:03,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:03,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference/checkm_data
[2024-01-24 13:18:03,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:03,192] [INFO] Task started: CheckM
[2024-01-24 13:18:03,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000189755.2_ASM18975v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000189755.2_ASM18975v3_genomic.fna/checkm_input GCF_000189755.2_ASM18975v3_genomic.fna/checkm_result
[2024-01-24 13:18:32,797] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:32,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:32,820] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:32,821] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:32,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000189755.2_ASM18975v3_genomic.fna/markers.fasta)
[2024-01-24 13:18:32,822] [INFO] Task started: Blastn
[2024-01-24 13:18:32,822] [INFO] Running command: blastn -query GCF_000189755.2_ASM18975v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c009227-3022-464b-ab71-16cb20357039/dqc_reference/reference_markers_gtdb.fasta -out GCF_000189755.2_ASM18975v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:33,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:33,626] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:33,626] [INFO] Target genome list was writen to GCF_000189755.2_ASM18975v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:33,640] [INFO] Task started: fastANI
[2024-01-24 13:18:33,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e43ea2c-cfc6-4f59-ba00-d5bfd50edaff/GCF_000189755.2_ASM18975v3_genomic.fna.gz --refList GCF_000189755.2_ASM18975v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000189755.2_ASM18975v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:42,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:42,100] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:42,101] [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_000189755.2	s__Desulfotomaculum nigrificans	100.0	1017	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	98.87	98.87	0.87	0.87	2	conclusive
GCF_900129195.1	s__Desulfotomaculum putei	80.6488	338	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002607855.1	s__Desulfotomaculum profundi	80.217	299	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315365.1	s__Desulfotomaculum hydrothermale	79.73	246	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002005145.1	s__Desulfotomaculum ferrireducens	79.4518	232	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016165.1	s__Desulfotomaculum reducens	78.7606	189	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215085.1	s__Desulfotomaculum ruminis	78.1216	220	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143605.1	s__Desulfotomaculum aquiferis	77.799	157	1017	d__Bacteria;p__Firmicutes_B;c__Desulfotomaculia;o__Desulfotomaculales;f__Desulfotomaculaceae;g__Desulfotomaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,106] [INFO] GTDB search result was written to GCF_000189755.2_ASM18975v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:42,107] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:42,113] [INFO] DFAST_QC result json was written to GCF_000189755.2_ASM18975v3_genomic.fna/dqc_result.json
[2024-01-24 13:18:42,113] [INFO] DFAST_QC completed!
[2024-01-24 13:18:42,113] [INFO] Total running time: 0h0m56s