[2023-06-08 10:40:33,471] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:40:33,473] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:40:33,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference
[2023-06-08 10:40:34,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:40:34,742] [INFO] Task started: Prodigal
[2023-06-08 10:40:34,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg18408a71-0d30-4a0f-9114-da25472d87f6/GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:40:39,366] [INFO] Task succeeded: Prodigal
[2023-06-08 10:40:39,367] [INFO] Task started: HMMsearch
[2023-06-08 10:40:39,367] [INFO] Running command: hmmsearch --tblout GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference/reference_markers.hmm GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:40:39,602] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:40:39,603] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg18408a71-0d30-4a0f-9114-da25472d87f6/GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 10:40:39,627] [INFO] Query marker FASTA was written to GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 10:40:39,628] [INFO] Task started: Blastn
[2023-06-08 10:40:39,628] [INFO] Running command: blastn -query GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference/reference_markers.fasta -out GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:40:40,117] [INFO] Task succeeded: Blastn
[2023-06-08 10:40:40,121] [INFO] Selected 20 target genomes.
[2023-06-08 10:40:40,121] [INFO] Target genome list was writen to GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 10:40:40,126] [INFO] Task started: fastANI
[2023-06-08 10:40:40,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg18408a71-0d30-4a0f-9114-da25472d87f6/GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:40:51,702] [INFO] Task succeeded: fastANI
[2023-06-08 10:40:51,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:40:51,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:40:51,705] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:40:51,705] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:40:51,705] [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 10:40:51,708] [INFO] DFAST Taxonomy check result was written to GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 10:40:51,709] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:40:51,709] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:40:51,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference/checkm_data
[2023-06-08 10:40:51,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:40:51,747] [INFO] Task started: CheckM
[2023-06-08 10:40:51,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 10:41:12,633] [INFO] Task succeeded: CheckM
[2023-06-08 10:41:12,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:41:12,655] [INFO] ===== Completeness check finished =====
[2023-06-08 10:41:12,655] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:41:12,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 10:41:12,656] [INFO] Task started: Blastn
[2023-06-08 10:41:12,656] [INFO] Running command: blastn -query GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec6c5a6-25c7-479f-9586-1bdde002ab65/dqc_reference/reference_markers_gtdb.fasta -out GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:41:13,131] [INFO] Task succeeded: Blastn
[2023-06-08 10:41:13,135] [INFO] Selected 8 target genomes.
[2023-06-08 10:41:13,135] [INFO] Target genome list was writen to GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:41:13,142] [INFO] Task started: fastANI
[2023-06-08 10:41:13,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg18408a71-0d30-4a0f-9114-da25472d87f6/GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:41:17,415] [INFO] Task succeeded: fastANI
[2023-06-08 10:41:17,427] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:41:17,427] [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_017626095.1	s__UBA2882 sp017626095	95.6935	364	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016297945.1	s__UBA2882 sp016297945	94.4984	336	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017387565.1	s__UBA2882 sp017387565	91.3403	356	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549665.1	s__UBA2882 sp900549665	79.7248	186	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.94	99.94	0.92	0.92	2	-
GCA_900317505.1	s__UBA2882 sp900317505	79.5396	182	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	99.59	99.48	0.89	0.88	4	-
GCA_017936785.1	s__UBA2882 sp017936785	78.0703	79	541	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2882	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:41:17,429] [INFO] GTDB search result was written to GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 10:41:17,430] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:41:17,432] [INFO] DFAST_QC result json was written to GCA_945876335.1_ERR1855549_bin.7_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 10:41:17,433] [INFO] DFAST_QC completed!
[2023-06-08 10:41:17,433] [INFO] Total running time: 0h0m44s