[2024-01-24 11:26:20,725] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference
[2024-01-24 11:26:21,944] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:21,944] [INFO] Task started: Prodigal
[2024-01-24 11:26:21,945] [INFO] Running command: gunzip -c /var/lib/cwl/stga60aae37-af47-4391-8925-a478b46ea4cf/GCF_014385085.1_ASM1438508v1_genomic.fna.gz | prodigal -d GCF_014385085.1_ASM1438508v1_genomic.fna/cds.fna -a GCF_014385085.1_ASM1438508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:28,669] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:28,669] [INFO] Task started: HMMsearch
[2024-01-24 11:26:28,669] [INFO] Running command: hmmsearch --tblout GCF_014385085.1_ASM1438508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference/reference_markers.hmm GCF_014385085.1_ASM1438508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:28,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:28,973] [INFO] Found 6/6 markers.
[2024-01-24 11:26:28,999] [INFO] Query marker FASTA was written to GCF_014385085.1_ASM1438508v1_genomic.fna/markers.fasta
[2024-01-24 11:26:29,000] [INFO] Task started: Blastn
[2024-01-24 11:26:29,000] [INFO] Running command: blastn -query GCF_014385085.1_ASM1438508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference/reference_markers.fasta -out GCF_014385085.1_ASM1438508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:29,630] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:29,634] [INFO] Selected 19 target genomes.
[2024-01-24 11:26:29,635] [INFO] Target genome list was writen to GCF_014385085.1_ASM1438508v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:29,663] [INFO] Task started: fastANI
[2024-01-24 11:26:29,663] [INFO] Running command: fastANI --query /var/lib/cwl/stga60aae37-af47-4391-8925-a478b46ea4cf/GCF_014385085.1_ASM1438508v1_genomic.fna.gz --refList GCF_014385085.1_ASM1438508v1_genomic.fna/target_genomes.txt --output GCF_014385085.1_ASM1438508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:39,821] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:39,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:39,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:39,833] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:39,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:39,834] [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
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	80.9445	87	870	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	80.6949	86	870	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	80.2121	52	870	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	77.9153	67	870	95	below_threshold
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	76.9333	67	870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:39,836] [INFO] DFAST Taxonomy check result was written to GCF_014385085.1_ASM1438508v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:39,836] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:39,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:39,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference/checkm_data
[2024-01-24 11:26:39,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:39,870] [INFO] Task started: CheckM
[2024-01-24 11:26:39,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385085.1_ASM1438508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385085.1_ASM1438508v1_genomic.fna/checkm_input GCF_014385085.1_ASM1438508v1_genomic.fna/checkm_result
[2024-01-24 11:27:05,844] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:05,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:05,864] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:05,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:05,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385085.1_ASM1438508v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:05,866] [INFO] Task started: Blastn
[2024-01-24 11:27:05,866] [INFO] Running command: blastn -query GCF_014385085.1_ASM1438508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg280a96e6-9d10-4bb4-9346-b99e6f5a3c35/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385085.1_ASM1438508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:06,940] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:06,944] [INFO] Selected 29 target genomes.
[2024-01-24 11:27:06,944] [INFO] Target genome list was writen to GCF_014385085.1_ASM1438508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:06,976] [INFO] Task started: fastANI
[2024-01-24 11:27:06,977] [INFO] Running command: fastANI --query /var/lib/cwl/stga60aae37-af47-4391-8925-a478b46ea4cf/GCF_014385085.1_ASM1438508v1_genomic.fna.gz --refList GCF_014385085.1_ASM1438508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385085.1_ASM1438508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:18,335] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:18,344] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:18,344] [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
GCA_014385085.1	s__Anaerotruncus sp014385085	100.0	869	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000154565.1	s__Anaerotruncus colihominis	80.623	87	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	-
GCF_900199635.1	s__Anaerotruncus massiliensis	80.2121	52	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	77.9149	67	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_000403395.2	s__Anaerotruncus sp000403395	77.6662	68	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.44	98.36	0.83	0.79	7	-
GCF_900186535.1	s__Anaerotruncus massiliensis_A	76.9333	67	870	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.01	98.01	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:18,346] [INFO] GTDB search result was written to GCF_014385085.1_ASM1438508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:18,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:18,348] [INFO] DFAST_QC result json was written to GCF_014385085.1_ASM1438508v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:18,349] [INFO] DFAST_QC completed!
[2024-01-24 11:27:18,349] [INFO] Total running time: 0h0m58s