[2023-07-01 04:51:17,981] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:51:17,987] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:51:17,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference
[2023-07-01 04:51:19,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:51:19,247] [INFO] Task started: Prodigal
[2023-07-01 04:51:19,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdba711a-7cd4-4724-a32c-a3d4949097ef/GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna.gz | prodigal -d GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/cds.fna -a GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:51:24,919] [INFO] Task succeeded: Prodigal
[2023-07-01 04:51:24,919] [INFO] Task started: HMMsearch
[2023-07-01 04:51:24,919] [INFO] Running command: hmmsearch --tblout GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference/reference_markers.hmm GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:51:25,134] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:51:25,135] [INFO] Found 6/6 markers.
[2023-07-01 04:51:25,157] [INFO] Query marker FASTA was written to GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/markers.fasta
[2023-07-01 04:51:25,157] [INFO] Task started: Blastn
[2023-07-01 04:51:25,157] [INFO] Running command: blastn -query GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/markers.fasta -db /var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference/reference_markers.fasta -out GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:51:25,782] [INFO] Task succeeded: Blastn
[2023-07-01 04:51:25,786] [INFO] Selected 28 target genomes.
[2023-07-01 04:51:25,787] [INFO] Target genome list was writen to GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/target_genomes.txt
[2023-07-01 04:51:25,788] [INFO] Task started: fastANI
[2023-07-01 04:51:25,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdba711a-7cd4-4724-a32c-a3d4949097ef/GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna.gz --refList GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/target_genomes.txt --output GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:51:43,003] [INFO] Task succeeded: fastANI
[2023-07-01 04:51:43,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:51:43,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:51:43,006] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:51:43,006] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:51:43,007] [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
--------------------------------------------------------------------------------
[2023-07-01 04:51:43,009] [INFO] DFAST Taxonomy check result was written to GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/tc_result.tsv
[2023-07-01 04:51:43,010] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:51:43,010] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:51:43,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference/checkm_data
[2023-07-01 04:51:43,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:51:43,041] [INFO] Task started: CheckM
[2023-07-01 04:51:43,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/checkm_input GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/checkm_result
[2023-07-01 04:52:06,842] [INFO] Task succeeded: CheckM
[2023-07-01 04:52:06,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.56%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:52:06,864] [INFO] ===== Completeness check finished =====
[2023-07-01 04:52:06,865] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:52:06,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/markers.fasta)
[2023-07-01 04:52:06,865] [INFO] Task started: Blastn
[2023-07-01 04:52:06,866] [INFO] Running command: blastn -query GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/markers.fasta -db /var/lib/cwl/stg98e4f2c5-9de8-46ec-aa77-fd9f12add217/dqc_reference/reference_markers_gtdb.fasta -out GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:52:07,772] [INFO] Task succeeded: Blastn
[2023-07-01 04:52:07,777] [INFO] Selected 13 target genomes.
[2023-07-01 04:52:07,777] [INFO] Target genome list was writen to GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:52:07,779] [INFO] Task started: fastANI
[2023-07-01 04:52:07,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdba711a-7cd4-4724-a32c-a3d4949097ef/GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna.gz --refList GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/target_genomes_gtdb.txt --output GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:52:13,291] [INFO] Task succeeded: fastANI
[2023-07-01 04:52:13,304] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:52:13,304] [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_903838355.1	s__Limnohabitans sp903838355	99.4887	179	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.89	99.57	0.92	0.68	43	conclusive
GCA_903844385.1	s__Limnohabitans sp903844385	82.9418	151	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.69	99.69	0.91	0.91	2	-
GCA_903887655.1	s__Limnohabitans sp903887655	81.4941	144	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.79	98.79	0.78	0.78	2	-
GCA_903864315.1	s__Limnohabitans sp903864315	80.9765	148	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.27	99.18	0.86	0.80	3	-
GCA_903865035.1	s__Limnohabitans sp903865035	77.4329	54	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.19	99.05	0.82	0.76	7	-
GCA_903933115.1	s__Limnohabitans sp903933115	76.8444	67	215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.52	99.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-07-01 04:52:13,306] [INFO] GTDB search result was written to GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/result_gtdb.tsv
[2023-07-01 04:52:13,307] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:52:13,309] [INFO] DFAST_QC result json was written to GCA_903916015.1_freshwater_MAG_---_KR5_bin-293_genomic.fna/dqc_result.json
[2023-07-01 04:52:13,309] [INFO] DFAST_QC completed!
[2023-07-01 04:52:13,310] [INFO] Total running time: 0h0m55s