[2024-01-24 13:10:19,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,288] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference
[2024-01-24 13:10:20,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,613] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgd00eb0ab-7e95-4146-88dc-ccf5ffc60b78/GCF_003010495.1_ASM301049v1_genomic.fna.gz | prodigal -d GCF_003010495.1_ASM301049v1_genomic.fna/cds.fna -a GCF_003010495.1_ASM301049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:27,340] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:27,340] [INFO] Task started: HMMsearch
[2024-01-24 13:10:27,341] [INFO] Running command: hmmsearch --tblout GCF_003010495.1_ASM301049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference/reference_markers.hmm GCF_003010495.1_ASM301049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:27,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:27,763] [INFO] Found 6/6 markers.
[2024-01-24 13:10:27,842] [INFO] Query marker FASTA was written to GCF_003010495.1_ASM301049v1_genomic.fna/markers.fasta
[2024-01-24 13:10:27,842] [INFO] Task started: Blastn
[2024-01-24 13:10:27,842] [INFO] Running command: blastn -query GCF_003010495.1_ASM301049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference/reference_markers.fasta -out GCF_003010495.1_ASM301049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:28,488] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:28,492] [INFO] Selected 6 target genomes.
[2024-01-24 13:10:28,493] [INFO] Target genome list was writen to GCF_003010495.1_ASM301049v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:28,495] [INFO] Task started: fastANI
[2024-01-24 13:10:28,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00eb0ab-7e95-4146-88dc-ccf5ffc60b78/GCF_003010495.1_ASM301049v1_genomic.fna.gz --refList GCF_003010495.1_ASM301049v1_genomic.fna/target_genomes.txt --output GCF_003010495.1_ASM301049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:33,396] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:33,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:33,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:33,402] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:33,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:33,402] [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=ATCC 25940	GCA_003010495.1	907	907	type	True	100.0	826	826	95	conclusive
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	99.9744	819	826	95	conclusive
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	82.3342	498	826	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	79.6071	371	826	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	79.4616	347	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:33,404] [INFO] DFAST Taxonomy check result was written to GCF_003010495.1_ASM301049v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:33,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:33,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:33,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference/checkm_data
[2024-01-24 13:10:33,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:33,432] [INFO] Task started: CheckM
[2024-01-24 13:10:33,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003010495.1_ASM301049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003010495.1_ASM301049v1_genomic.fna/checkm_input GCF_003010495.1_ASM301049v1_genomic.fna/checkm_result
[2024-01-24 13:10:59,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:59,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:59,672] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:59,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:59,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003010495.1_ASM301049v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:59,674] [INFO] Task started: Blastn
[2024-01-24 13:10:59,674] [INFO] Running command: blastn -query GCF_003010495.1_ASM301049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab5d657-9656-4b2f-b677-2266c8ad5182/dqc_reference/reference_markers_gtdb.fasta -out GCF_003010495.1_ASM301049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:00,530] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:00,534] [INFO] Selected 7 target genomes.
[2024-01-24 13:11:00,534] [INFO] Target genome list was writen to GCF_003010495.1_ASM301049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:00,544] [INFO] Task started: fastANI
[2024-01-24 13:11:00,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00eb0ab-7e95-4146-88dc-ccf5ffc60b78/GCF_003010495.1_ASM301049v1_genomic.fna.gz --refList GCF_003010495.1_ASM301049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003010495.1_ASM301049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:05,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:05,118] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:05,118] [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	100.0	826	826	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	90.9969	630	826	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	90.3949	461	826	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	87.9244	446	826	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	82.5418	492	826	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	82.4656	501	826	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	82.2697	424	826	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:05,119] [INFO] GTDB search result was written to GCF_003010495.1_ASM301049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:05,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:05,122] [INFO] DFAST_QC result json was written to GCF_003010495.1_ASM301049v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:05,123] [INFO] DFAST_QC completed!
[2024-01-24 13:11:05,123] [INFO] Total running time: 0h0m46s