[2023-06-13 10:49:43,681] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:49:43,683] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:49:43,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference
[2023-06-13 10:49:44,939] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:49:44,940] [INFO] Task started: Prodigal
[2023-06-13 10:49:44,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfedefa1-c229-457e-aea0-2cd572c1fa6e/GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:49:48,484] [INFO] Task succeeded: Prodigal
[2023-06-13 10:49:48,484] [INFO] Task started: HMMsearch
[2023-06-13 10:49:48,485] [INFO] Running command: hmmsearch --tblout GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference/reference_markers.hmm GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:49:48,702] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:49:48,704] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcfedefa1-c229-457e-aea0-2cd572c1fa6e/GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 10:49:48,740] [INFO] Query marker FASTA was written to GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 10:49:48,741] [INFO] Task started: Blastn
[2023-06-13 10:49:48,741] [INFO] Running command: blastn -query GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference/reference_markers.fasta -out GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:49:49,226] [INFO] Task succeeded: Blastn
[2023-06-13 10:49:49,232] [INFO] Selected 14 target genomes.
[2023-06-13 10:49:49,232] [INFO] Target genome list was writen to GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 10:49:49,236] [INFO] Task started: fastANI
[2023-06-13 10:49:49,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfedefa1-c229-457e-aea0-2cd572c1fa6e/GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:49:57,300] [INFO] Task succeeded: fastANI
[2023-06-13 10:49:57,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:49:57,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:49:57,303] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:49:57,303] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:49:57,303] [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
--------------------------------------------------------------------------------
[2023-06-13 10:49:57,305] [INFO] DFAST Taxonomy check result was written to GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 10:49:57,307] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:49:57,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:49:57,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference/checkm_data
[2023-06-13 10:49:57,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:49:57,339] [INFO] Task started: CheckM
[2023-06-13 10:49:57,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 10:50:16,361] [INFO] Task succeeded: CheckM
[2023-06-13 10:50:16,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:50:16,405] [INFO] ===== Completeness check finished =====
[2023-06-13 10:50:16,406] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:50:16,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 10:50:16,407] [INFO] Task started: Blastn
[2023-06-13 10:50:16,407] [INFO] Running command: blastn -query GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg46668334-42c0-4a3a-982e-075d02e443d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:50:16,941] [INFO] Task succeeded: Blastn
[2023-06-13 10:50:16,947] [INFO] Selected 15 target genomes.
[2023-06-13 10:50:16,947] [INFO] Target genome list was writen to GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:50:16,952] [INFO] Task started: fastANI
[2023-06-13 10:50:16,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfedefa1-c229-457e-aea0-2cd572c1fa6e/GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:50:26,354] [INFO] Task succeeded: fastANI
[2023-06-13 10:50:26,366] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:50:26,366] [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_910579515.1	s__UBA3402 sp910579515	98.3305	362	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910585435.1	s__UBA3402 sp910585435	78.4404	145	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588325.1	s__UBA3402 sp910588325	78.3686	128	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588505.1	s__UBA3402 sp910588505	76.6735	62	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575585.1	s__UBA3402 sp910575585	76.6469	79	399	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	99.89	99.85	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-13 10:50:26,369] [INFO] GTDB search result was written to GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 10:50:26,370] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:50:26,374] [INFO] DFAST_QC result json was written to GCA_947063965.1_ERR9465724_bin.10_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 10:50:26,374] [INFO] DFAST_QC completed!
[2023-06-13 10:50:26,374] [INFO] Total running time: 0h0m43s