[2023-06-30 06:11:24,876] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:11:24,878] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:11:24,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference
[2023-06-30 06:11:26,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:11:26,918] [INFO] Task started: Prodigal
[2023-06-30 06:11:26,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg70a19d2c-6d78-4a7c-967a-99ebe732a63a/GCA_900753335.1_ERS396359_79_genomic.fna.gz | prodigal -d GCA_900753335.1_ERS396359_79_genomic.fna/cds.fna -a GCA_900753335.1_ERS396359_79_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:11:30,521] [INFO] Task succeeded: Prodigal
[2023-06-30 06:11:30,521] [INFO] Task started: HMMsearch
[2023-06-30 06:11:30,522] [INFO] Running command: hmmsearch --tblout GCA_900753335.1_ERS396359_79_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference/reference_markers.hmm GCA_900753335.1_ERS396359_79_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:11:30,782] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:11:30,783] [INFO] Found 6/6 markers.
[2023-06-30 06:11:30,810] [INFO] Query marker FASTA was written to GCA_900753335.1_ERS396359_79_genomic.fna/markers.fasta
[2023-06-30 06:11:30,811] [INFO] Task started: Blastn
[2023-06-30 06:11:30,811] [INFO] Running command: blastn -query GCA_900753335.1_ERS396359_79_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference/reference_markers.fasta -out GCA_900753335.1_ERS396359_79_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:11:32,215] [INFO] Task succeeded: Blastn
[2023-06-30 06:11:32,219] [INFO] Selected 10 target genomes.
[2023-06-30 06:11:32,221] [INFO] Target genome list was writen to GCA_900753335.1_ERS396359_79_genomic.fna/target_genomes.txt
[2023-06-30 06:11:32,230] [INFO] Task started: fastANI
[2023-06-30 06:11:32,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg70a19d2c-6d78-4a7c-967a-99ebe732a63a/GCA_900753335.1_ERS396359_79_genomic.fna.gz --refList GCA_900753335.1_ERS396359_79_genomic.fna/target_genomes.txt --output GCA_900753335.1_ERS396359_79_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:11:37,069] [INFO] Task succeeded: fastANI
[2023-06-30 06:11:37,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:11:37,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:11:37,083] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:11:37,084] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 06:11:37,084] [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
Megamonas funiformis	strain=YIT 11815	GCA_000245775.1	437897	437897	type	True	93.8932	495	589	95	below_threshold
Megamonas funiformis	strain=JCM 14723	GCA_010669225.1	437897	437897	type	True	93.7573	504	589	95	below_threshold
Megamonas hypermegale	strain=DSM 1672	GCA_000423385.1	158847	158847	type	True	82.0673	355	589	95	below_threshold
Megamonas hypermegale	strain=NCTC10570	GCA_900187035.1	158847	158847	type	True	81.9655	368	589	95	below_threshold
Pectinatus brassicae	strain=DSM 24661	GCA_014201835.1	862415	862415	type	True	76.7846	67	589	95	below_threshold
Propionispira arboris	strain=DSM 2179	GCA_900109225.1	84035	84035	type	True	76.4948	60	589	95	below_threshold
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	76.2851	60	589	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 06:11:37,087] [INFO] DFAST Taxonomy check result was written to GCA_900753335.1_ERS396359_79_genomic.fna/tc_result.tsv
[2023-06-30 06:11:37,088] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:11:37,088] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:11:37,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference/checkm_data
[2023-06-30 06:11:37,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:11:37,125] [INFO] Task started: CheckM
[2023-06-30 06:11:37,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900753335.1_ERS396359_79_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900753335.1_ERS396359_79_genomic.fna/checkm_input GCA_900753335.1_ERS396359_79_genomic.fna/checkm_result
[2023-06-30 06:11:56,507] [INFO] Task succeeded: CheckM
[2023-06-30 06:11:56,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:11:56,530] [INFO] ===== Completeness check finished =====
[2023-06-30 06:11:56,531] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:11:56,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900753335.1_ERS396359_79_genomic.fna/markers.fasta)
[2023-06-30 06:11:56,531] [INFO] Task started: Blastn
[2023-06-30 06:11:56,532] [INFO] Running command: blastn -query GCA_900753335.1_ERS396359_79_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ad461ce-f21a-46dd-ad6c-0bf1d4566a7b/dqc_reference/reference_markers_gtdb.fasta -out GCA_900753335.1_ERS396359_79_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:11:57,347] [INFO] Task succeeded: Blastn
[2023-06-30 06:11:57,351] [INFO] Selected 20 target genomes.
[2023-06-30 06:11:57,352] [INFO] Target genome list was writen to GCA_900753335.1_ERS396359_79_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:11:57,364] [INFO] Task started: fastANI
[2023-06-30 06:11:57,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg70a19d2c-6d78-4a7c-967a-99ebe732a63a/GCA_900753335.1_ERS396359_79_genomic.fna.gz --refList GCA_900753335.1_ERS396359_79_genomic.fna/target_genomes_gtdb.txt --output GCA_900753335.1_ERS396359_79_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:12:05,890] [INFO] Task succeeded: fastANI
[2023-06-30 06:12:05,905] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:12:05,906] [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_900556715.1	s__Megamonas sp900556715	99.5255	246	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	99.82	99.65	0.90	0.83	3	conclusive
GCF_010669225.1	s__Megamonas funiformis	93.7434	504	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	97.89	97.23	0.89	0.80	26	-
GCF_900187035.1	s__Megamonas hypermegale	81.9343	369	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	98.37	97.31	0.90	0.84	6	-
GCA_002314325.1	s__Megamonas hypermegale_A	79.226	148	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554895.1	s__Megamonas gallistercoris	77.8466	149	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	98.29	98.29	0.76	0.76	2	-
GCA_902363205.1	s__CABIZH01 sp902363205	77.1921	52	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__CABIZH01	95.0	97.61	97.54	0.87	0.81	4	-
GCF_014201835.1	s__Pectinatus brassicae	76.7893	68	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900109225.1	s__Propionispira arboris	76.4654	61	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
GCF_015732155.1	s__Pectinatus sottacetonis	76.3266	61	589	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:12:05,908] [INFO] GTDB search result was written to GCA_900753335.1_ERS396359_79_genomic.fna/result_gtdb.tsv
[2023-06-30 06:12:05,909] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:12:05,912] [INFO] DFAST_QC result json was written to GCA_900753335.1_ERS396359_79_genomic.fna/dqc_result.json
[2023-06-30 06:12:05,913] [INFO] DFAST_QC completed!
[2023-06-30 06:12:05,913] [INFO] Total running time: 0h0m41s