[2023-06-14 01:47:38,999] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:47:39,001] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:47:39,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference
[2023-06-14 01:47:40,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:47:40,264] [INFO] Task started: Prodigal
[2023-06-14 01:47:40,264] [INFO] Running command: gunzip -c /var/lib/cwl/stg218b2162-0d25-423f-abc0-82e04f95617c/GCA_022774445.1_ASM2277444v1_genomic.fna.gz | prodigal -d GCA_022774445.1_ASM2277444v1_genomic.fna/cds.fna -a GCA_022774445.1_ASM2277444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:47:44,359] [INFO] Task succeeded: Prodigal
[2023-06-14 01:47:44,359] [INFO] Task started: HMMsearch
[2023-06-14 01:47:44,359] [INFO] Running command: hmmsearch --tblout GCA_022774445.1_ASM2277444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference/reference_markers.hmm GCA_022774445.1_ASM2277444v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:47:44,613] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:47:44,614] [INFO] Found 6/6 markers.
[2023-06-14 01:47:44,639] [INFO] Query marker FASTA was written to GCA_022774445.1_ASM2277444v1_genomic.fna/markers.fasta
[2023-06-14 01:47:44,640] [INFO] Task started: Blastn
[2023-06-14 01:47:44,640] [INFO] Running command: blastn -query GCA_022774445.1_ASM2277444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference/reference_markers.fasta -out GCA_022774445.1_ASM2277444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:47:45,246] [INFO] Task succeeded: Blastn
[2023-06-14 01:47:45,250] [INFO] Selected 6 target genomes.
[2023-06-14 01:47:45,251] [INFO] Target genome list was writen to GCA_022774445.1_ASM2277444v1_genomic.fna/target_genomes.txt
[2023-06-14 01:47:45,252] [INFO] Task started: fastANI
[2023-06-14 01:47:45,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg218b2162-0d25-423f-abc0-82e04f95617c/GCA_022774445.1_ASM2277444v1_genomic.fna.gz --refList GCA_022774445.1_ASM2277444v1_genomic.fna/target_genomes.txt --output GCA_022774445.1_ASM2277444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:47:49,109] [INFO] Task succeeded: fastANI
[2023-06-14 01:47:49,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:47:49,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:47:49,120] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-06-14 01:47:49,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-14 01:47:49,120] [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
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	98.7304	460	475	95	conclusive
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	98.684	461	475	95	conclusive
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	82.6402	371	475	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	79.6162	259	475	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	79.477	265	475	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:47:49,123] [INFO] DFAST Taxonomy check result was written to GCA_022774445.1_ASM2277444v1_genomic.fna/tc_result.tsv
[2023-06-14 01:47:49,124] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:47:49,124] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:47:49,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference/checkm_data
[2023-06-14 01:47:49,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:47:49,148] [INFO] Task started: CheckM
[2023-06-14 01:47:49,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022774445.1_ASM2277444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022774445.1_ASM2277444v1_genomic.fna/checkm_input GCA_022774445.1_ASM2277444v1_genomic.fna/checkm_result
[2023-06-14 01:48:08,841] [INFO] Task succeeded: CheckM
[2023-06-14 01:48:08,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:48:08,867] [INFO] ===== Completeness check finished =====
[2023-06-14 01:48:08,868] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:48:08,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022774445.1_ASM2277444v1_genomic.fna/markers.fasta)
[2023-06-14 01:48:08,869] [INFO] Task started: Blastn
[2023-06-14 01:48:08,869] [INFO] Running command: blastn -query GCA_022774445.1_ASM2277444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60a12aec-71f3-4616-a301-5f668568ec93/dqc_reference/reference_markers_gtdb.fasta -out GCA_022774445.1_ASM2277444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:09,694] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:09,699] [INFO] Selected 7 target genomes.
[2023-06-14 01:48:09,699] [INFO] Target genome list was writen to GCA_022774445.1_ASM2277444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:48:09,702] [INFO] Task started: fastANI
[2023-06-14 01:48:09,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg218b2162-0d25-423f-abc0-82e04f95617c/GCA_022774445.1_ASM2277444v1_genomic.fna.gz --refList GCA_022774445.1_ASM2277444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022774445.1_ASM2277444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:48:13,214] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:13,222] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:48:13,222] [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_003010495.1	s__Megasphaera elsdenii	98.7368	460	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	conclusive
GCF_000417505.1	s__Megasphaera sp000417505	91.0854	440	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_902388315.1	s__Megasphaera sp902388315	90.4612	355	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCA_900548635.1	s__Megasphaera sp900548635	87.7392	340	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCA_900539295.1	s__Megasphaera sp900539295	82.7252	377	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001546855.1	s__Megasphaera sp001546855	82.6505	381	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
GCA_002319965.1	s__Megasphaera sp002319965	82.5453	311	475	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-14 01:48:13,224] [INFO] GTDB search result was written to GCA_022774445.1_ASM2277444v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:48:13,224] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:48:13,227] [INFO] DFAST_QC result json was written to GCA_022774445.1_ASM2277444v1_genomic.fna/dqc_result.json
[2023-06-14 01:48:13,227] [INFO] DFAST_QC completed!
[2023-06-14 01:48:13,228] [INFO] Total running time: 0h0m34s