[2023-06-13 08:51:48,728] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:51:48,730] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:51:48,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference
[2023-06-13 08:51:51,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:51:51,506] [INFO] Task started: Prodigal
[2023-06-13 08:51:51,506] [INFO] Running command: gunzip -c /var/lib/cwl/stga9041ccd-1991-45f4-8cdc-b70dcd452825/GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:51:58,784] [INFO] Task succeeded: Prodigal
[2023-06-13 08:51:58,784] [INFO] Task started: HMMsearch
[2023-06-13 08:51:58,784] [INFO] Running command: hmmsearch --tblout GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference/reference_markers.hmm GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:51:58,958] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:51:58,959] [INFO] Found 6/6 markers.
[2023-06-13 08:51:58,978] [INFO] Query marker FASTA was written to GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 08:51:58,978] [INFO] Task started: Blastn
[2023-06-13 08:51:58,978] [INFO] Running command: blastn -query GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference/reference_markers.fasta -out GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:51:59,895] [INFO] Task succeeded: Blastn
[2023-06-13 08:51:59,904] [INFO] Selected 9 target genomes.
[2023-06-13 08:51:59,904] [INFO] Target genome list was writen to GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 08:51:59,928] [INFO] Task started: fastANI
[2023-06-13 08:51:59,928] [INFO] Running command: fastANI --query /var/lib/cwl/stga9041ccd-1991-45f4-8cdc-b70dcd452825/GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:04,132] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:04,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:04,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:04,141] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 08:52:04,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 08:52:04,142] [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
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000687595.1	1690	1694	type	True	96.3196	563	682	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=LMG 11569	GCA_000741295.1	1690	1694	type	True	96.2736	562	682	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_002706665.1	1690	1694	type	True	96.2303	572	682	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	96.191	555	682	95	conclusive
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	93.4912	574	682	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.6221	339	682	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.7934	322	682	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.7031	103	682	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.7668	100	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:04,145] [INFO] DFAST Taxonomy check result was written to GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 08:52:04,146] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:04,146] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:04,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference/checkm_data
[2023-06-13 08:52:04,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:04,170] [INFO] Task started: CheckM
[2023-06-13 08:52:04,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 08:52:32,473] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:32,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:32,495] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:32,495] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:32,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 08:52:32,496] [INFO] Task started: Blastn
[2023-06-13 08:52:32,496] [INFO] Running command: blastn -query GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg56011d8a-6f04-43ae-8622-af2af6a41940/dqc_reference/reference_markers_gtdb.fasta -out GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:34,013] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:34,016] [INFO] Selected 9 target genomes.
[2023-06-13 08:52:34,016] [INFO] Target genome list was writen to GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:34,050] [INFO] Task started: fastANI
[2023-06-13 08:52:34,050] [INFO] Running command: fastANI --query /var/lib/cwl/stga9041ccd-1991-45f4-8cdc-b70dcd452825/GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:52:38,792] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:38,800] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 08:52:38,801] [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_000741295.1	s__Bifidobacterium globosum	96.2736	562	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.22	96.02	0.90	0.78	79	inconclusive
GCF_004155535.1	s__Bifidobacterium pseudolongum_C	95.1684	593	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000771225.1	s__Bifidobacterium pseudolongum	93.475	572	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.10	98.38	0.94	0.92	10	-
GCF_000741135.1	s__Bifidobacterium choerinum	83.401	479	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_003952025.1	s__Bifidobacterium castoris	83.3845	489	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286915.1	s__Bifidobacterium italicum	83.2251	486	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741575.1	s__Bifidobacterium cuniculi	81.3765	413	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003952945.1	s__Bifidobacterium samirii	80.8744	334	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	80.495	321	682	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:52:38,803] [INFO] GTDB search result was written to GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 08:52:38,803] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:52:38,806] [INFO] DFAST_QC result json was written to GCA_947644155.1_SRR15633975_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 08:52:38,807] [INFO] DFAST_QC completed!
[2023-06-13 08:52:38,807] [INFO] Total running time: 0h0m50s