[2023-06-05 09:25:22,359] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:25:22,362] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:25:22,362] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference
[2023-06-05 09:25:23,789] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:25:23,790] [INFO] Task started: Prodigal
[2023-06-05 09:25:23,791] [INFO] Running command: gunzip -c /var/lib/cwl/stgc406d2ce-6c98-4aac-a6b7-b31d4768fbf1/GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:25:26,705] [INFO] Task succeeded: Prodigal
[2023-06-05 09:25:26,705] [INFO] Task started: HMMsearch
[2023-06-05 09:25:26,706] [INFO] Running command: hmmsearch --tblout GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference/reference_markers.hmm GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:25:26,948] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:25:26,949] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc406d2ce-6c98-4aac-a6b7-b31d4768fbf1/GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-05 09:25:26,972] [INFO] Query marker FASTA was written to GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-05 09:25:26,973] [INFO] Task started: Blastn
[2023-06-05 09:25:26,973] [INFO] Running command: blastn -query GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference/reference_markers.fasta -out GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:27,558] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:27,562] [INFO] Selected 15 target genomes.
[2023-06-05 09:25:27,563] [INFO] Target genome list was writen to GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-05 09:25:27,568] [INFO] Task started: fastANI
[2023-06-05 09:25:27,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgc406d2ce-6c98-4aac-a6b7-b31d4768fbf1/GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:25:32,636] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:32,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:25:32,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:25:32,643] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:25:32,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:25:32,644] [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
Gemella haemolysans	strain=ATCC 10379	GCA_000173915.1	1379	1379	suspected-type	True	92.8881	205	485	95	below_threshold
Gemella haemolysans	strain=CCUG 37985T	GCA_008692995.1	1379	1379	suspected-type	True	92.7567	205	485	95	below_threshold
Gemella sanguinis	strain=ATCC 700632	GCA_000701685.1	84135	84135	type	True	81.4408	135	485	95	below_threshold
Gemella morbillorum	strain=FDAARGOS_1501	GCA_020097435.1	29391	29391	type	True	80.632	119	485	95	below_threshold
Gemella morbillorum	strain=NCTC11323	GCA_900476045.1	29391	29391	type	True	80.576	117	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:25:32,646] [INFO] DFAST Taxonomy check result was written to GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-05 09:25:32,646] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:25:32,646] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:25:32,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference/checkm_data
[2023-06-05 09:25:32,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:25:32,671] [INFO] Task started: CheckM
[2023-06-05 09:25:32,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-05 09:25:49,829] [INFO] Task succeeded: CheckM
[2023-06-05 09:25:49,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.12%
Contamintation: 9.72%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:25:49,853] [INFO] ===== Completeness check finished =====
[2023-06-05 09:25:49,853] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:25:49,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-05 09:25:49,854] [INFO] Task started: Blastn
[2023-06-05 09:25:49,854] [INFO] Running command: blastn -query GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e98bee2-9c04-42c9-982d-ce53101199d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:50,649] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:50,653] [INFO] Selected 11 target genomes.
[2023-06-05 09:25:50,653] [INFO] Target genome list was writen to GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:25:50,662] [INFO] Task started: fastANI
[2023-06-05 09:25:50,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgc406d2ce-6c98-4aac-a6b7-b31d4768fbf1/GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:25:54,033] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:54,046] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:25:54,046] [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_001553035.1	s__Gemella haemolysans_B	96.1444	214	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	97.70	97.59	0.85	0.81	4	conclusive
GCF_000173915.1	s__Gemella haemolysans	92.8881	205	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.96	99.96	0.99	0.99	3	-
GCA_900766305.1	s__Gemella sp900766305	91.7989	204	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002871655.1	s__Gemella sp002871655	87.0633	191	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	98.42	98.42	0.93	0.93	2	-
GCF_012273215.1	s__Gemella haemolysans_A	86.2818	195	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.95	99.95	0.99	0.99	2	-
GCF_901873445.1	s__Gemella haemolysans_C	86.2363	190	485	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:25:54,049] [INFO] GTDB search result was written to GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-05 09:25:54,050] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:25:54,054] [INFO] DFAST_QC result json was written to GCA_916049735.1_ERR2764813_bin.8_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-05 09:25:54,054] [INFO] DFAST_QC completed!
[2023-06-05 09:25:54,054] [INFO] Total running time: 0h0m32s