[2024-01-24 13:30:12,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:12,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:12,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference
[2024-01-24 13:30:13,310] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:13,311] [INFO] Task started: Prodigal
[2024-01-24 13:30:13,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a4c7a96-a2e0-4018-b57d-196433cfcf02/GCF_009735625.1_ASM973562v1_genomic.fna.gz | prodigal -d GCF_009735625.1_ASM973562v1_genomic.fna/cds.fna -a GCF_009735625.1_ASM973562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:21,950] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:21,951] [INFO] Task started: HMMsearch
[2024-01-24 13:30:21,951] [INFO] Running command: hmmsearch --tblout GCF_009735625.1_ASM973562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference/reference_markers.hmm GCF_009735625.1_ASM973562v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:22,198] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:22,199] [INFO] Found 6/6 markers.
[2024-01-24 13:30:22,234] [INFO] Query marker FASTA was written to GCF_009735625.1_ASM973562v1_genomic.fna/markers.fasta
[2024-01-24 13:30:22,235] [INFO] Task started: Blastn
[2024-01-24 13:30:22,235] [INFO] Running command: blastn -query GCF_009735625.1_ASM973562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference/reference_markers.fasta -out GCF_009735625.1_ASM973562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:22,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:22,832] [INFO] Selected 7 target genomes.
[2024-01-24 13:30:22,832] [INFO] Target genome list was writen to GCF_009735625.1_ASM973562v1_genomic.fna/target_genomes.txt
[2024-01-24 13:30:22,985] [INFO] Task started: fastANI
[2024-01-24 13:30:22,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4c7a96-a2e0-4018-b57d-196433cfcf02/GCF_009735625.1_ASM973562v1_genomic.fna.gz --refList GCF_009735625.1_ASM973562v1_genomic.fna/target_genomes.txt --output GCF_009735625.1_ASM973562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:28,754] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:28,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:28,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:28,765] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:30:28,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:28,766] [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
Moorella glycerini	strain=DSM 11254	GCA_009735625.1	55779	55779	type	True	100.0	1185	1185	95	conclusive
Moorella stamsii	strain=DSM 26217	GCA_002995805.1	1266720	1266720	type	True	93.2924	746	1185	95	below_threshold
Moorella mulderi	strain=DSM 14980	GCA_001594015.1	202604	202604	type	True	93.0304	720	1185	95	below_threshold
Moorella humiferrea	strain=DSM 23265	GCA_002995755.1	676965	676965	type	True	82.1791	525	1185	95	below_threshold
Moorella thermoacetica	strain=DSM 2955	GCA_001267435.1	1525	1525	type	True	81.2544	504	1185	95	below_threshold
Moorella thermoacetica	strain=ATCC 35608	GCA_008121885.1	1525	1525	type	True	81.0333	495	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:28,767] [INFO] DFAST Taxonomy check result was written to GCF_009735625.1_ASM973562v1_genomic.fna/tc_result.tsv
[2024-01-24 13:30:28,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:28,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:28,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference/checkm_data
[2024-01-24 13:30:28,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:28,807] [INFO] Task started: CheckM
[2024-01-24 13:30:28,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009735625.1_ASM973562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009735625.1_ASM973562v1_genomic.fna/checkm_input GCF_009735625.1_ASM973562v1_genomic.fna/checkm_result
[2024-01-24 13:30:58,604] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:58,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:58,636] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:58,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:58,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009735625.1_ASM973562v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:58,637] [INFO] Task started: Blastn
[2024-01-24 13:30:58,637] [INFO] Running command: blastn -query GCF_009735625.1_ASM973562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg186ebaa3-e7e1-4855-a7ba-3b7eeb3b4e7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009735625.1_ASM973562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:59,467] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:59,473] [INFO] Selected 7 target genomes.
[2024-01-24 13:30:59,473] [INFO] Target genome list was writen to GCF_009735625.1_ASM973562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:59,625] [INFO] Task started: fastANI
[2024-01-24 13:30:59,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4c7a96-a2e0-4018-b57d-196433cfcf02/GCF_009735625.1_ASM973562v1_genomic.fna.gz --refList GCF_009735625.1_ASM973562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009735625.1_ASM973562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:05,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:05,500] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:05,501] [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_009735625.1	s__Moorella glycerini	100.0	1184	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002995805.1	s__Moorella stamsii	93.2825	747	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	99.99	99.99	0.99	0.99	2	-
GCF_001594015.1	s__Moorella mulderi	93.0304	720	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.265	N/A	N/A	N/A	N/A	1	-
GCF_006538365.1	s__Moorella sp006538365	89.6227	684	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	99.18	99.18	0.87	0.87	2	-
GCF_002995755.1	s__Moorella humiferrea	82.1461	527	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	97.49	97.49	0.85	0.85	2	-
GCF_003116935.1	s__Moorella sp003116935	80.6711	555	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383405.1	s__Moorella sp002383405	80.1208	348	1185	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Moorellales;f__Moorellaceae;g__Moorella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:05,503] [INFO] GTDB search result was written to GCF_009735625.1_ASM973562v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:05,504] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:05,508] [INFO] DFAST_QC result json was written to GCF_009735625.1_ASM973562v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:05,509] [INFO] DFAST_QC completed!
[2024-01-24 13:31:05,509] [INFO] Total running time: 0h0m53s