[2023-06-08 07:24:28,430] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:24:28,432] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:24:28,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference
[2023-06-08 07:24:30,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:24:30,135] [INFO] Task started: Prodigal
[2023-06-08 07:24:30,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bc951ae-d230-48c6-9634-b2a56af13404/GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:24:34,516] [INFO] Task succeeded: Prodigal
[2023-06-08 07:24:34,517] [INFO] Task started: HMMsearch
[2023-06-08 07:24:34,517] [INFO] Running command: hmmsearch --tblout GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference/reference_markers.hmm GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:24:34,868] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:24:34,869] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4bc951ae-d230-48c6-9634-b2a56af13404/GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 07:24:34,893] [INFO] Query marker FASTA was written to GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 07:24:34,894] [INFO] Task started: Blastn
[2023-06-08 07:24:34,894] [INFO] Running command: blastn -query GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference/reference_markers.fasta -out GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:36,266] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:36,270] [INFO] Selected 23 target genomes.
[2023-06-08 07:24:36,271] [INFO] Target genome list was writen to GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 07:24:36,293] [INFO] Task started: fastANI
[2023-06-08 07:24:36,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc951ae-d230-48c6-9634-b2a56af13404/GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:24:53,001] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:53,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:24:53,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:24:53,004] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:24:53,004] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 07:24:53,004] [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
--------------------------------------------------------------------------------
[2023-06-08 07:24:53,007] [INFO] DFAST Taxonomy check result was written to GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 07:24:53,008] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:24:53,009] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:24:53,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference/checkm_data
[2023-06-08 07:24:53,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:24:53,041] [INFO] Task started: CheckM
[2023-06-08 07:24:53,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 07:25:15,005] [INFO] Task succeeded: CheckM
[2023-06-08 07:25:15,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 07:25:15,043] [INFO] ===== Completeness check finished =====
[2023-06-08 07:25:15,044] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:25:15,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 07:25:15,045] [INFO] Task started: Blastn
[2023-06-08 07:25:15,045] [INFO] Running command: blastn -query GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg20e4a0fc-4255-4551-b3d3-54c5df0b12e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:25:15,890] [INFO] Task succeeded: Blastn
[2023-06-08 07:25:15,895] [INFO] Selected 15 target genomes.
[2023-06-08 07:25:15,895] [INFO] Target genome list was writen to GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:25:15,905] [INFO] Task started: fastANI
[2023-06-08 07:25:15,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bc951ae-d230-48c6-9634-b2a56af13404/GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:25:22,963] [INFO] Task succeeded: fastANI
[2023-06-08 07:25:23,000] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:25:23,000] [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_016293365.1	s__Bulleidia sp016293365	99.0	430	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014610835.1	s__Bulleidia sp900539965	77.7515	82	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.38	98.19	0.87	0.84	4	-
GCA_900315065.1	s__Bulleidia sp900315065	77.1714	82	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.99	99.99	0.97	0.97	2	-
GCA_905201565.1	s__Bulleidia sp905201565	77.1538	54	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761625.1	s__Bulleidia sp902761625	76.9081	56	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539825.1	s__Bulleidia sp017539825	76.5292	53	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000701725.1	s__Bulleidia sp000701725	76.5257	55	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.69	96.78	0.88	0.87	6	-
GCA_902766435.1	s__Bulleidia sp902766435	76.3241	52	479	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:25:23,003] [INFO] GTDB search result was written to GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 07:25:23,004] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:25:23,007] [INFO] DFAST_QC result json was written to GCA_945489235.1_SRR7188235_bin.40_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 07:25:23,007] [INFO] DFAST_QC completed!
[2023-06-08 07:25:23,007] [INFO] Total running time: 0h0m55s