[2024-01-25 18:04:20,701] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:20,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:20,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference
[2024-01-25 18:04:21,852] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:21,852] [INFO] Task started: Prodigal
[2024-01-25 18:04:21,853] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c5d0432-5996-4af2-ae50-e6851964a1a7/GCF_030812885.1_ASM3081288v1_genomic.fna.gz | prodigal -d GCF_030812885.1_ASM3081288v1_genomic.fna/cds.fna -a GCF_030812885.1_ASM3081288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:27,507] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:27,507] [INFO] Task started: HMMsearch
[2024-01-25 18:04:27,507] [INFO] Running command: hmmsearch --tblout GCF_030812885.1_ASM3081288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference/reference_markers.hmm GCF_030812885.1_ASM3081288v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:27,727] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:27,728] [INFO] Found 6/6 markers.
[2024-01-25 18:04:27,751] [INFO] Query marker FASTA was written to GCF_030812885.1_ASM3081288v1_genomic.fna/markers.fasta
[2024-01-25 18:04:27,751] [INFO] Task started: Blastn
[2024-01-25 18:04:27,751] [INFO] Running command: blastn -query GCF_030812885.1_ASM3081288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference/reference_markers.fasta -out GCF_030812885.1_ASM3081288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:28,361] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:28,364] [INFO] Selected 26 target genomes.
[2024-01-25 18:04:28,364] [INFO] Target genome list was writen to GCF_030812885.1_ASM3081288v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:28,375] [INFO] Task started: fastANI
[2024-01-25 18:04:28,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c5d0432-5996-4af2-ae50-e6851964a1a7/GCF_030812885.1_ASM3081288v1_genomic.fna.gz --refList GCF_030812885.1_ASM3081288v1_genomic.fna/target_genomes.txt --output GCF_030812885.1_ASM3081288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:44,634] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:44,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:44,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:44,638] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:04:44,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:04:44,639] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	79.1287	52	810	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	78.9241	50	810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:44,640] [INFO] DFAST Taxonomy check result was written to GCF_030812885.1_ASM3081288v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:44,640] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:44,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:44,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference/checkm_data
[2024-01-25 18:04:44,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:44,668] [INFO] Task started: CheckM
[2024-01-25 18:04:44,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030812885.1_ASM3081288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030812885.1_ASM3081288v1_genomic.fna/checkm_input GCF_030812885.1_ASM3081288v1_genomic.fna/checkm_result
[2024-01-25 18:05:06,453] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:06,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:06,480] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:06,480] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:06,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030812885.1_ASM3081288v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:06,480] [INFO] Task started: Blastn
[2024-01-25 18:05:06,480] [INFO] Running command: blastn -query GCF_030812885.1_ASM3081288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95f7d168-c064-4c69-a1c7-e358adfa0de3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030812885.1_ASM3081288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:07,609] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:07,612] [INFO] Selected 23 target genomes.
[2024-01-25 18:05:07,612] [INFO] Target genome list was writen to GCF_030812885.1_ASM3081288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:07,623] [INFO] Task started: fastANI
[2024-01-25 18:05:07,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c5d0432-5996-4af2-ae50-e6851964a1a7/GCF_030812885.1_ASM3081288v1_genomic.fna.gz --refList GCF_030812885.1_ASM3081288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030812885.1_ASM3081288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:18,722] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:18,728] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:18,728] [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_003014445.1	s__Stomatobaculum naviforme	98.7513	677	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	100.00	100.00	0.99	0.99	3	conclusive
GCA_002892395.1	s__Stomatobaculum sp002892395	79.8724	174	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242235.1	s__Stomatobaculum longum	78.3148	150	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	97.78	97.78	0.96	0.96	2	-
GCA_905370385.1	s__Stomatobaculum longum_A	77.9862	116	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793685.1	s__Stomatobaculum sp902793685	77.6026	123	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	97.67	97.61	0.89	0.87	3	-
GCA_902780465.1	s__Stomatobaculum sp902780465	77.2326	101	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	97.77	97.33	0.79	0.76	4	-
GCA_902766175.1	s__Stomatobaculum sp902766175	76.9463	145	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766415.1	s__Stomatobaculum sp902766415	76.4685	61	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:18,730] [INFO] GTDB search result was written to GCF_030812885.1_ASM3081288v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:18,730] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:18,732] [INFO] DFAST_QC result json was written to GCF_030812885.1_ASM3081288v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:18,732] [INFO] DFAST_QC completed!
[2024-01-25 18:05:18,732] [INFO] Total running time: 0h0m58s