[2023-06-28 03:25:04,498] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:25:04,500] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:25:04,500] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference
[2023-06-28 03:25:05,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:25:05,945] [INFO] Task started: Prodigal
[2023-06-28 03:25:05,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cdf455d-d4c0-4d82-820a-122a93229d0a/GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:25:08,478] [INFO] Task succeeded: Prodigal
[2023-06-28 03:25:08,478] [INFO] Task started: HMMsearch
[2023-06-28 03:25:08,479] [INFO] Running command: hmmsearch --tblout GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference/reference_markers.hmm GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:25:08,656] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:25:08,657] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9cdf455d-d4c0-4d82-820a-122a93229d0a/GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 03:25:08,671] [INFO] Query marker FASTA was written to GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 03:25:08,671] [INFO] Task started: Blastn
[2023-06-28 03:25:08,671] [INFO] Running command: blastn -query GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference/reference_markers.fasta -out GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:09,249] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:09,253] [INFO] Selected 16 target genomes.
[2023-06-28 03:25:09,253] [INFO] Target genome list was writen to GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 03:25:09,257] [INFO] Task started: fastANI
[2023-06-28 03:25:09,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cdf455d-d4c0-4d82-820a-122a93229d0a/GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:25:19,399] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:19,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:25:19,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:25:19,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:25:19,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:25:19,402] [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
--------------------------------------------------------------------------------
[2023-06-28 03:25:19,404] [INFO] DFAST Taxonomy check result was written to GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 03:25:19,405] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:25:19,405] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:25:19,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference/checkm_data
[2023-06-28 03:25:19,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:25:19,422] [INFO] Task started: CheckM
[2023-06-28 03:25:19,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 03:25:35,914] [INFO] Task succeeded: CheckM
[2023-06-28 03:25:35,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 26.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:25:35,934] [INFO] ===== Completeness check finished =====
[2023-06-28 03:25:35,934] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:25:35,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 03:25:35,935] [INFO] Task started: Blastn
[2023-06-28 03:25:35,935] [INFO] Running command: blastn -query GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d0f327-9425-467e-8208-5851bdad311e/dqc_reference/reference_markers_gtdb.fasta -out GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:36,444] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:36,456] [INFO] Selected 12 target genomes.
[2023-06-28 03:25:36,456] [INFO] Target genome list was writen to GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:25:36,468] [INFO] Task started: fastANI
[2023-06-28 03:25:36,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cdf455d-d4c0-4d82-820a-122a93229d0a/GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:25:40,917] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:40,929] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:25:40,930] [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_905478555.1	s__GCA-002697625 sp905478555	96.1107	155	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	conclusive
GCA_018647945.1	s__GCA-002697625 sp018647945	81.2489	105	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_902514225.1	s__GCA-002697625 sp902514225	80.0428	74	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710495.1	s__GCA-002697625 sp002710495	78.8064	87	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018695965.1	s__GCA-002697625 sp018695965	78.7967	90	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	98.45	97.65	0.78	0.72	6	-
GCA_002697625.1	s__GCA-002697625 sp002697625	78.2064	90	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696275.1	s__GCA-002697625 sp002696275	77.8204	81	177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:25:40,933] [INFO] GTDB search result was written to GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 03:25:40,933] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:25:40,936] [INFO] DFAST_QC result json was written to GCA_913046115.1_ERR599122_bin.123_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 03:25:40,936] [INFO] DFAST_QC completed!
[2023-06-28 03:25:40,937] [INFO] Total running time: 0h0m36s