[2023-06-14 01:26:38,269] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:26:38,273] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:26:38,273] [INFO] DQC Reference Directory: /var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference
[2023-06-14 01:26:39,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:26:39,560] [INFO] Task started: Prodigal
[2023-06-14 01:26:39,561] [INFO] Running command: gunzip -c /var/lib/cwl/stgef04a1a6-e527-42a7-bbfd-59a0be319c34/GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:26:52,320] [INFO] Task succeeded: Prodigal
[2023-06-14 01:26:52,320] [INFO] Task started: HMMsearch
[2023-06-14 01:26:52,320] [INFO] Running command: hmmsearch --tblout GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference/reference_markers.hmm GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:26:52,548] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:26:52,549] [INFO] Found 6/6 markers.
[2023-06-14 01:26:52,573] [INFO] Query marker FASTA was written to GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-14 01:26:52,574] [INFO] Task started: Blastn
[2023-06-14 01:26:52,574] [INFO] Running command: blastn -query GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference/reference_markers.fasta -out GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:26:53,189] [INFO] Task succeeded: Blastn
[2023-06-14 01:26:53,193] [INFO] Selected 22 target genomes.
[2023-06-14 01:26:53,193] [INFO] Target genome list was writen to GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:26:53,204] [INFO] Task started: fastANI
[2023-06-14 01:26:53,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgef04a1a6-e527-42a7-bbfd-59a0be319c34/GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:27:07,056] [INFO] Task succeeded: fastANI
[2023-06-14 01:27:07,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:27:07,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:27:07,060] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:27:07,060] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:27:07,060] [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
--------------------------------------------------------------------------------
[2023-06-14 01:27:07,062] [INFO] DFAST Taxonomy check result was written to GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:27:07,063] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:27:07,063] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:27:07,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference/checkm_data
[2023-06-14 01:27:07,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:27:07,095] [INFO] Task started: CheckM
[2023-06-14 01:27:07,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-14 01:27:47,650] [INFO] Task succeeded: CheckM
[2023-06-14 01:27:47,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:27:47,673] [INFO] ===== Completeness check finished =====
[2023-06-14 01:27:47,673] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:27:47,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:27:47,674] [INFO] Task started: Blastn
[2023-06-14 01:27:47,674] [INFO] Running command: blastn -query GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgac74d72f-dc8a-4ef0-ad5b-be82ce8ab21b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:27:48,541] [INFO] Task succeeded: Blastn
[2023-06-14 01:27:48,546] [INFO] Selected 20 target genomes.
[2023-06-14 01:27:48,546] [INFO] Target genome list was writen to GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:27:48,556] [INFO] Task started: fastANI
[2023-06-14 01:27:48,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgef04a1a6-e527-42a7-bbfd-59a0be319c34/GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:27:56,739] [INFO] Task succeeded: fastANI
[2023-06-14 01:27:56,759] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:27:56,760] [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_002491945.1	s__CAG-485 sp002491945	99.8804	627	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.81	98.93	0.94	0.91	9	conclusive
GCA_910577585.1	s__CAG-485 sp910577585	78.864	269	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801595.1	s__CAG-485 sp014801595	78.6729	151	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.47	97.47	0.83	0.83	2	-
GCA_014802625.1	s__CAG-485 sp014802625	78.2175	153	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014802425.1	s__CAG-485 sp014802425	78.1482	213	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014801585.1	s__CAG-485 sp014801585	78.0164	96	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.82	97.82	0.79	0.79	2	-
GCA_014803765.1	s__CAG-485 sp014803765	77.3509	64	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	98.16	98.16	0.67	0.67	2	-
GCA_009775375.1	s__CAG-485 sp009775375	77.1815	72	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.86	99.86	0.92	0.92	2	-
GCA_910578385.1	s__CAG-485 sp910578385	77.0309	100	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760885.1	s__CAG-485 sp900760885	76.9921	76	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935045.1	s__CAG-485 sp017935045	76.7554	61	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800685.1	s__CAG-485 sp014800685	76.7405	52	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	97.88	97.69	0.85	0.84	4	-
GCA_900542185.1	s__CAG-485 sp900542185	76.6772	65	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014800895.1	s__CAG-485 sp014800895	76.6459	57	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491165.1	s__CAG-485 sp002491165	76.566	63	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	99.22	96.16	0.89	0.85	9	-
GCA_910584525.1	s__CAG-485 sp910584525	76.4292	80	717	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-485	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:27:56,761] [INFO] GTDB search result was written to GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:27:56,762] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:27:56,765] [INFO] DFAST_QC result json was written to GCA_947178635.1_SRR13713024_bin.5_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:27:56,765] [INFO] DFAST_QC completed!
[2023-06-14 01:27:56,765] [INFO] Total running time: 0h1m18s