[2023-06-13 05:50:02,378] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:50:02,380] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:50:02,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference
[2023-06-13 05:50:03,730] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:50:03,731] [INFO] Task started: Prodigal
[2023-06-13 05:50:03,731] [INFO] Running command: gunzip -c /var/lib/cwl/stgda9eef9d-50d9-4a8c-9477-ad427258efa0/GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:50:09,852] [INFO] Task succeeded: Prodigal
[2023-06-13 05:50:09,853] [INFO] Task started: HMMsearch
[2023-06-13 05:50:09,853] [INFO] Running command: hmmsearch --tblout GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference/reference_markers.hmm GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:50:10,069] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:50:10,071] [INFO] Found 6/6 markers.
[2023-06-13 05:50:10,093] [INFO] Query marker FASTA was written to GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 05:50:10,094] [INFO] Task started: Blastn
[2023-06-13 05:50:10,094] [INFO] Running command: blastn -query GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference/reference_markers.fasta -out GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:10,713] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:10,717] [INFO] Selected 14 target genomes.
[2023-06-13 05:50:10,717] [INFO] Target genome list was writen to GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 05:50:10,720] [INFO] Task started: fastANI
[2023-06-13 05:50:10,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgda9eef9d-50d9-4a8c-9477-ad427258efa0/GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:50:18,954] [INFO] Task succeeded: fastANI
[2023-06-13 05:50:18,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:50:18,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:50:18,967] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 05:50:18,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 05:50:18,968] [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
Actinotignum sanguinis	strain=DSM 26039	GCA_003957255.1	1445614	1445614	type	True	97.529	567	649	95	conclusive
Actinotignum timonense	strain=type strain: Marseille-P2803	GCA_900155575.1	1870995	1870995	type	True	89.7217	608	649	95	below_threshold
Actinotignum schaalii	strain=DSM 15541	GCA_000429205.1	59505	59505	type	True	89.6194	583	649	95	below_threshold
Actinotignum schaalii	strain=CCUG 27420	GCA_000724605.1	59505	59505	type	True	89.61	588	649	95	below_threshold
Actinobaculum massiliense	strain=FC3	GCA_001457435.1	202789	202789	neotype	True	76.7772	99	649	95	below_threshold
Actinobaculum suis	strain=DSM 20639	GCA_900102025.1	1657	1657	type	True	76.5132	76	649	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 05:50:18,972] [INFO] DFAST Taxonomy check result was written to GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 05:50:18,973] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:50:18,973] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:50:18,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference/checkm_data
[2023-06-13 05:50:18,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:50:18,998] [INFO] Task started: CheckM
[2023-06-13 05:50:18,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 05:50:42,502] [INFO] Task succeeded: CheckM
[2023-06-13 05:50:42,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:50:42,522] [INFO] ===== Completeness check finished =====
[2023-06-13 05:50:42,523] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:50:42,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 05:50:42,524] [INFO] Task started: Blastn
[2023-06-13 05:50:42,524] [INFO] Running command: blastn -query GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5a1912-06d2-4cee-9b09-9d5c798d00cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:43,394] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:43,399] [INFO] Selected 11 target genomes.
[2023-06-13 05:50:43,399] [INFO] Target genome list was writen to GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:50:43,403] [INFO] Task started: fastANI
[2023-06-13 05:50:43,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgda9eef9d-50d9-4a8c-9477-ad427258efa0/GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:50:48,157] [INFO] Task succeeded: fastANI
[2023-06-13 05:50:48,164] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:50:48,164] [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_003957255.1	s__Actinotignum sanguinis	97.529	567	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000411135.1	s__Actinotignum schaalii_A	92.5057	589	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155575.1	s__Actinotignum timonense	89.7217	608	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	99.14	98.55	0.97	0.96	4	-
GCF_000724605.1	s__Actinotignum schaalii	89.61	588	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinotignum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001457435.1	s__Actinobaculum massiliense	76.7551	100	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinobaculum	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900604955.1	s__Neoactinobaculum massilliense	76.3317	55	649	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Neoactinobaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:50:48,166] [INFO] GTDB search result was written to GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 05:50:48,167] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:50:48,170] [INFO] DFAST_QC result json was written to GCA_947253365.1_SRR17635715_bin.31_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 05:50:48,170] [INFO] DFAST_QC completed!
[2023-06-13 05:50:48,170] [INFO] Total running time: 0h0m46s