[2023-06-08 11:16:42,665] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:16:42,667] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:16:42,667] [INFO] DQC Reference Directory: /var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference
[2023-06-08 11:16:44,183] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:44,184] [INFO] Task started: Prodigal
[2023-06-08 11:16:44,184] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcfdabb5-a308-47e5-950f-5e703b1952df/GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:47,501] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:47,501] [INFO] Task started: HMMsearch
[2023-06-08 11:16:47,501] [INFO] Running command: hmmsearch --tblout GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference/reference_markers.hmm GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:47,662] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:47,664] [INFO] Found 6/6 markers.
[2023-06-08 11:16:47,680] [INFO] Query marker FASTA was written to GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:16:47,681] [INFO] Task started: Blastn
[2023-06-08 11:16:47,681] [INFO] Running command: blastn -query GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference/reference_markers.fasta -out GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:48,307] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:48,311] [INFO] Selected 24 target genomes.
[2023-06-08 11:16:48,311] [INFO] Target genome list was writen to GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:16:48,313] [INFO] Task started: fastANI
[2023-06-08 11:16:48,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcfdabb5-a308-47e5-950f-5e703b1952df/GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:17:00,577] [INFO] Task succeeded: fastANI
[2023-06-08 11:17:00,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:17:00,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:17:00,580] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:17:00,580] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:17:00,580] [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 11:17:00,582] [INFO] DFAST Taxonomy check result was written to GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:17:00,582] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:17:00,583] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:17:00,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference/checkm_data
[2023-06-08 11:17:00,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:17:00,603] [INFO] Task started: CheckM
[2023-06-08 11:17:00,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:17:17,066] [INFO] Task succeeded: CheckM
[2023-06-08 11:17:17,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.37%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-08 11:17:17,088] [INFO] ===== Completeness check finished =====
[2023-06-08 11:17:17,089] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:17:17,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:17:17,089] [INFO] Task started: Blastn
[2023-06-08 11:17:17,089] [INFO] Running command: blastn -query GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb78aa270-f258-4846-b1cd-35ef20494ca9/dqc_reference/reference_markers_gtdb.fasta -out GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:17:18,179] [INFO] Task succeeded: Blastn
[2023-06-08 11:17:18,183] [INFO] Selected 11 target genomes.
[2023-06-08 11:17:18,183] [INFO] Target genome list was writen to GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:17:18,186] [INFO] Task started: fastANI
[2023-06-08 11:17:18,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcfdabb5-a308-47e5-950f-5e703b1952df/GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:17:22,191] [INFO] Task succeeded: fastANI
[2023-06-08 11:17:22,201] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 11:17:22,201] [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_017429325.1	s__Faecousia sp017429325	80.5606	169	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540945.1	s__Faecousia sp017540945	80.4477	218	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.32	98.32	0.76	0.76	2	-
GCA_017541995.1	s__Faecousia sp017541995	80.3303	223	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519005.1	s__Faecousia sp017519005	80.2415	220	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.84	97.84	0.75	0.75	2	-
GCA_016292255.1	s__Faecousia sp016292255	80.0784	230	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282135.1	s__Faecousia sp016282135	80.057	209	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767915.1	s__Faecousia sp902767915	79.839	171	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.86	97.78	0.84	0.82	3	-
GCA_017614755.1	s__Faecousia sp017614755	79.5427	188	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017419715.1	s__Faecousia sp017419715	79.4275	175	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017543225.1	s__Faecousia sp017543225	78.7203	155	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017612935.1	s__Faecousia sp017612935	78.2602	125	407	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:17:22,203] [INFO] GTDB search result was written to GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:17:22,204] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:17:22,207] [INFO] DFAST_QC result json was written to GCA_945487445.1_SRR7188236_bin.37_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:17:22,207] [INFO] DFAST_QC completed!
[2023-06-08 11:17:22,207] [INFO] Total running time: 0h0m40s