[2024-01-24 10:57:19,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:19,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:19,737] [INFO] DQC Reference Directory: /var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference
[2024-01-24 10:57:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,298] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,299] [INFO] Running command: gunzip -c /var/lib/cwl/stgde258ebb-558c-4252-8690-0e8c478e7005/GCF_001953175.1_ASM195317v1_genomic.fna.gz | prodigal -d GCF_001953175.1_ASM195317v1_genomic.fna/cds.fna -a GCF_001953175.1_ASM195317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:27,960] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:27,960] [INFO] Task started: HMMsearch
[2024-01-24 10:57:27,961] [INFO] Running command: hmmsearch --tblout GCF_001953175.1_ASM195317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference/reference_markers.hmm GCF_001953175.1_ASM195317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:28,205] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:28,206] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgde258ebb-558c-4252-8690-0e8c478e7005/GCF_001953175.1_ASM195317v1_genomic.fna.gz]
[2024-01-24 10:57:28,233] [INFO] Query marker FASTA was written to GCF_001953175.1_ASM195317v1_genomic.fna/markers.fasta
[2024-01-24 10:57:28,233] [INFO] Task started: Blastn
[2024-01-24 10:57:28,234] [INFO] Running command: blastn -query GCF_001953175.1_ASM195317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference/reference_markers.fasta -out GCF_001953175.1_ASM195317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:30,113] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:30,119] [INFO] Selected 11 target genomes.
[2024-01-24 10:57:30,119] [INFO] Target genome list was writen to GCF_001953175.1_ASM195317v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:30,317] [INFO] Task started: fastANI
[2024-01-24 10:57:30,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgde258ebb-558c-4252-8690-0e8c478e7005/GCF_001953175.1_ASM195317v1_genomic.fna.gz --refList GCF_001953175.1_ASM195317v1_genomic.fna/target_genomes.txt --output GCF_001953175.1_ASM195317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:37,777] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:37,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:37,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:37,791] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:37,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:37,792] [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
Dehalogenimonas formicexedens	strain=NSZ-14	GCA_001953175.1	1839801	1839801	type	True	100.0	691	697	95	conclusive
Dehalogenimonas alkenigignens	strain=IP3-3	GCA_001466665.1	1217799	1217799	type	True	82.0841	210	697	95	below_threshold
Candidatus Dehalogenimonas etheniformans	strain=GP	GCA_014672715.2	1536648	1536648	type	True	81.4375	377	697	95	below_threshold
Candidatus Dehalogenimonas etheniformans	strain=GP	GCA_002878295.2	1536648	1536648	type	True	81.3843	372	697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:37,793] [INFO] DFAST Taxonomy check result was written to GCF_001953175.1_ASM195317v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:37,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:37,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:37,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference/checkm_data
[2024-01-24 10:57:37,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:37,819] [INFO] Task started: CheckM
[2024-01-24 10:57:37,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001953175.1_ASM195317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001953175.1_ASM195317v1_genomic.fna/checkm_input GCF_001953175.1_ASM195317v1_genomic.fna/checkm_result
[2024-01-24 10:58:01,230] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:01,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,248] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:01,249] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:01,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001953175.1_ASM195317v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:01,249] [INFO] Task started: Blastn
[2024-01-24 10:58:01,250] [INFO] Running command: blastn -query GCF_001953175.1_ASM195317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeea5cebd-bd28-4454-b645-3a2115ea6b9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001953175.1_ASM195317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:02,124] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:02,127] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:02,127] [INFO] Target genome list was writen to GCF_001953175.1_ASM195317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:02,184] [INFO] Task started: fastANI
[2024-01-24 10:58:02,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgde258ebb-558c-4252-8690-0e8c478e7005/GCF_001953175.1_ASM195317v1_genomic.fna.gz --refList GCF_001953175.1_ASM195317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001953175.1_ASM195317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:08,795] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:08,806] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:08,806] [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_001953175.1	s__Dehalogenimonas formicexedens	100.0	692	697	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001466665.1	s__Dehalogenimonas alkenigignens	82.0974	208	697	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	99.11	99.11	0.94	0.94	2	-
GCF_014672715.2	s__Dehalogenimonas sp002878295	81.4195	378	697	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000143165.1	s__Dehalogenimonas lykanthroporepellens	77.6134	82	697	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001005265.1	s__Dehalogenimonas sp001005265	77.3736	63	697	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__Dehalococcoidaceae;g__Dehalogenimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:08,808] [INFO] GTDB search result was written to GCF_001953175.1_ASM195317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:08,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:08,811] [INFO] DFAST_QC result json was written to GCF_001953175.1_ASM195317v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:08,811] [INFO] DFAST_QC completed!
[2024-01-24 10:58:08,811] [INFO] Total running time: 0h0m49s