[2024-01-24 13:01:24,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference
[2024-01-24 13:01:26,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:26,121] [INFO] Task started: Prodigal
[2024-01-24 13:01:26,121] [INFO] Running command: gunzip -c /var/lib/cwl/stg664634e2-8dac-4198-89a9-1a2d166ff580/GCF_005405185.1_ASM540518v1_genomic.fna.gz | prodigal -d GCF_005405185.1_ASM540518v1_genomic.fna/cds.fna -a GCF_005405185.1_ASM540518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:31,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:31,929] [INFO] Task started: HMMsearch
[2024-01-24 13:01:31,929] [INFO] Running command: hmmsearch --tblout GCF_005405185.1_ASM540518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference/reference_markers.hmm GCF_005405185.1_ASM540518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:32,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:32,247] [INFO] Found 6/6 markers.
[2024-01-24 13:01:32,304] [INFO] Query marker FASTA was written to GCF_005405185.1_ASM540518v1_genomic.fna/markers.fasta
[2024-01-24 13:01:32,311] [INFO] Task started: Blastn
[2024-01-24 13:01:32,311] [INFO] Running command: blastn -query GCF_005405185.1_ASM540518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference/reference_markers.fasta -out GCF_005405185.1_ASM540518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:32,934] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:32,937] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:32,938] [INFO] Target genome list was writen to GCF_005405185.1_ASM540518v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:32,974] [INFO] Task started: fastANI
[2024-01-24 13:01:32,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg664634e2-8dac-4198-89a9-1a2d166ff580/GCF_005405185.1_ASM540518v1_genomic.fna.gz --refList GCF_005405185.1_ASM540518v1_genomic.fna/target_genomes.txt --output GCF_005405185.1_ASM540518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:39,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:39,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:39,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:39,476] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:39,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:39,477] [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
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	100.0	828	836	95	conclusive
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	90.8956	706	836	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	90.7981	708	836	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	90.6914	698	836	95	below_threshold
Secundilactobacillus yichangensis	strain=F79-211-2	GCA_016861565.1	2799580	2799580	type	True	81.7747	482	836	95	below_threshold
Secundilactobacillus pentosiphilus	strain=IWT25	GCA_002217985.1	1714682	1714682	type	True	81.6671	451	836	95	below_threshold
Secundilactobacillus mixtipabuli	strain=IWT30	GCA_002217925.1	1435342	1435342	type	True	81.464	448	836	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	81.1205	457	836	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	79.3979	190	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:39,478] [INFO] DFAST Taxonomy check result was written to GCF_005405185.1_ASM540518v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:39,479] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:39,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:39,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference/checkm_data
[2024-01-24 13:01:39,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:39,513] [INFO] Task started: CheckM
[2024-01-24 13:01:39,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405185.1_ASM540518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405185.1_ASM540518v1_genomic.fna/checkm_input GCF_005405185.1_ASM540518v1_genomic.fna/checkm_result
[2024-01-24 13:02:05,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:05,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:05,192] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:05,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:05,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405185.1_ASM540518v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:05,194] [INFO] Task started: Blastn
[2024-01-24 13:02:05,194] [INFO] Running command: blastn -query GCF_005405185.1_ASM540518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c93989-ec04-48d5-949d-4f08dbc12d6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405185.1_ASM540518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:06,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:06,021] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:06,022] [INFO] Target genome list was writen to GCF_005405185.1_ASM540518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:06,029] [INFO] Task started: fastANI
[2024-01-24 13:02:06,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg664634e2-8dac-4198-89a9-1a2d166ff580/GCF_005405185.1_ASM540518v1_genomic.fna.gz --refList GCF_005405185.1_ASM540518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405185.1_ASM540518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:10,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:10,788] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:10,789] [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_005405185.1	s__Secundilactobacillus sp005405185	100.0	828	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002217945.1	s__Secundilactobacillus silagei	90.758	710	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	-
GCF_016861565.1	s__Secundilactobacillus sp016861565	81.7747	482	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217985.1	s__Secundilactobacillus pentosiphilus	81.683	450	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.11	97.11	0.89	0.89	2	-
GCF_002583405.1	s__Secundilactobacillus silagincola	81.5652	481	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	81.461	449	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641075.1	s__Secundilactobacillus sp012641075	81.1311	457	836	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:10,791] [INFO] GTDB search result was written to GCF_005405185.1_ASM540518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:10,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:10,795] [INFO] DFAST_QC result json was written to GCF_005405185.1_ASM540518v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:10,796] [INFO] DFAST_QC completed!
[2024-01-24 13:02:10,796] [INFO] Total running time: 0h0m46s