[2024-01-24 13:09:34,020] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,024] [INFO] DQC Reference Directory: /var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference
[2024-01-24 13:09:35,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,374] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,374] [INFO] Running command: gunzip -c /var/lib/cwl/stgf23b1e1f-3f76-4b4f-9781-571c2d476bc8/GCF_002201475.1_ASM220147v1_genomic.fna.gz | prodigal -d GCF_002201475.1_ASM220147v1_genomic.fna/cds.fna -a GCF_002201475.1_ASM220147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:46,719] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:46,720] [INFO] Task started: HMMsearch
[2024-01-24 13:09:46,720] [INFO] Running command: hmmsearch --tblout GCF_002201475.1_ASM220147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference/reference_markers.hmm GCF_002201475.1_ASM220147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:47,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:47,005] [INFO] Found 6/6 markers.
[2024-01-24 13:09:47,037] [INFO] Query marker FASTA was written to GCF_002201475.1_ASM220147v1_genomic.fna/markers.fasta
[2024-01-24 13:09:47,037] [INFO] Task started: Blastn
[2024-01-24 13:09:47,038] [INFO] Running command: blastn -query GCF_002201475.1_ASM220147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference/reference_markers.fasta -out GCF_002201475.1_ASM220147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:47,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:47,700] [INFO] Selected 15 target genomes.
[2024-01-24 13:09:47,700] [INFO] Target genome list was writen to GCF_002201475.1_ASM220147v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:47,707] [INFO] Task started: fastANI
[2024-01-24 13:09:47,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgf23b1e1f-3f76-4b4f-9781-571c2d476bc8/GCF_002201475.1_ASM220147v1_genomic.fna.gz --refList GCF_002201475.1_ASM220147v1_genomic.fna/target_genomes.txt --output GCF_002201475.1_ASM220147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:57,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:57,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:57,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:57,370] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:57,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:57,370] [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
Acutalibacter muris	strain=KB18	GCA_002201475.1	1796620	1796620	type	True	100.0	1263	1267	95	conclusive
Acutalibacter muris	strain=KB18	GCA_016697365.1	1796620	1796620	type	True	100.0	1263	1267	95	conclusive
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.3915	65	1267	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.9828	58	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:57,372] [INFO] DFAST Taxonomy check result was written to GCF_002201475.1_ASM220147v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:57,373] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:57,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:57,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference/checkm_data
[2024-01-24 13:09:57,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:57,412] [INFO] Task started: CheckM
[2024-01-24 13:09:57,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002201475.1_ASM220147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002201475.1_ASM220147v1_genomic.fna/checkm_input GCF_002201475.1_ASM220147v1_genomic.fna/checkm_result
[2024-01-24 13:10:30,361] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:30,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:30,379] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:30,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:30,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002201475.1_ASM220147v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:30,380] [INFO] Task started: Blastn
[2024-01-24 13:10:30,380] [INFO] Running command: blastn -query GCF_002201475.1_ASM220147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge059bc79-3d74-41e4-84a1-c2a6e6337491/dqc_reference/reference_markers_gtdb.fasta -out GCF_002201475.1_ASM220147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:31,366] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:31,369] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:31,369] [INFO] Target genome list was writen to GCF_002201475.1_ASM220147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:31,377] [INFO] Task started: fastANI
[2024-01-24 13:10:31,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgf23b1e1f-3f76-4b4f-9781-571c2d476bc8/GCF_002201475.1_ASM220147v1_genomic.fna.gz --refList GCF_002201475.1_ASM220147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002201475.1_ASM220147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:38,998] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:39,007] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:39,007] [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_002201475.1	s__Acutalibacter muris	100.0	1264	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.54	97.39	0.89	0.78	6	conclusive
GCA_910584745.1	s__Acutalibacter sp910584745	87.1929	715	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009917305.1	s__Acutalibacter muris_A	85.2383	699	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009917525.1	s__Acutalibacter sp009917525	82.7419	647	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612555.1	s__Acutalibacter sp003612555	80.7223	427	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587835.1	s__Acutalibacter sp910587835	80.1127	397	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587995.1	s__Acutalibacter sp910587995	78.9606	324	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435395.1	s__Acutalibacter ornithocaccae	78.1004	242	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.90	97.28	0.83	0.80	5	-
GCA_019115285.1	s__Acutalibacter pullistercoris	77.8717	193	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755895.1	s__Acutalibacter sp900755895	77.0136	138	1267	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	96.98	96.98	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:39,009] [INFO] GTDB search result was written to GCF_002201475.1_ASM220147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:39,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:39,013] [INFO] DFAST_QC result json was written to GCF_002201475.1_ASM220147v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:39,013] [INFO] DFAST_QC completed!
[2024-01-24 13:10:39,013] [INFO] Total running time: 0h1m5s