[2023-06-07 20:07:53,076] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:07:53,079] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:07:53,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference
[2023-06-07 20:07:55,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:07:55,339] [INFO] Task started: Prodigal
[2023-06-07 20:07:55,339] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2ddf859-9ba9-4216-b9c7-9d27e38e75c8/GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:08:02,748] [INFO] Task succeeded: Prodigal
[2023-06-07 20:08:02,749] [INFO] Task started: HMMsearch
[2023-06-07 20:08:02,749] [INFO] Running command: hmmsearch --tblout GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference/reference_markers.hmm GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:08:03,008] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:08:03,010] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc2ddf859-9ba9-4216-b9c7-9d27e38e75c8/GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 20:08:03,028] [INFO] Query marker FASTA was written to GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 20:08:03,028] [INFO] Task started: Blastn
[2023-06-07 20:08:03,029] [INFO] Running command: blastn -query GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference/reference_markers.fasta -out GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:03,671] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:03,676] [INFO] Selected 19 target genomes.
[2023-06-07 20:08:03,676] [INFO] Target genome list was writen to GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 20:08:03,678] [INFO] Task started: fastANI
[2023-06-07 20:08:03,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ddf859-9ba9-4216-b9c7-9d27e38e75c8/GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:08:15,801] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:15,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:08:15,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:08:15,804] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:08:15,804] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 20:08:15,804] [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
--------------------------------------------------------------------------------
[2023-06-07 20:08:15,806] [INFO] DFAST Taxonomy check result was written to GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 20:08:15,807] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:08:15,808] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:08:15,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference/checkm_data
[2023-06-07 20:08:15,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:08:15,838] [INFO] Task started: CheckM
[2023-06-07 20:08:15,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 20:08:44,287] [INFO] Task succeeded: CheckM
[2023-06-07 20:08:44,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:08:44,310] [INFO] ===== Completeness check finished =====
[2023-06-07 20:08:44,311] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:08:44,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 20:08:44,312] [INFO] Task started: Blastn
[2023-06-07 20:08:44,312] [INFO] Running command: blastn -query GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d8c7564-382a-478b-8e13-a6dada9a04a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:45,136] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:45,142] [INFO] Selected 16 target genomes.
[2023-06-07 20:08:45,142] [INFO] Target genome list was writen to GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:08:45,151] [INFO] Task started: fastANI
[2023-06-07 20:08:45,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2ddf859-9ba9-4216-b9c7-9d27e38e75c8/GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:08:50,673] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:50,684] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:08:50,685] [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_004551865.1	s__Onthomorpha sp004551865	98.577	280	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	98.58	98.00	0.85	0.80	9	conclusive
GCA_016296345.1	s__Onthomorpha sp016296345	91.9995	252	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	97.30	97.30	0.84	0.84	2	-
GCA_900545215.1	s__Onthomorpha sp900545215	77.3388	98	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	98.29	98.29	0.90	0.90	2	-
GCA_900546465.1	s__Onthomorpha sp900546465	77.312	95	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	98.11	98.11	0.81	0.81	2	-
GCA_017632095.1	s__Onthomorpha sp017632095	77.0104	57	300	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__Onthomorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 20:08:50,687] [INFO] GTDB search result was written to GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 20:08:50,688] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:08:50,691] [INFO] DFAST_QC result json was written to GCA_945831765.1_SRR5976187_bin.43_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 20:08:50,692] [INFO] DFAST_QC completed!
[2023-06-07 20:08:50,692] [INFO] Total running time: 0h0m58s