[2023-06-29 23:52:25,394] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:52:25,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:52:25,396] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference
[2023-06-29 23:52:26,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:52:26,567] [INFO] Task started: Prodigal
[2023-06-29 23:52:26,567] [INFO] Running command: gunzip -c /var/lib/cwl/stgf083d16b-d774-47bc-85b6-e5c7d3c8adda/GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna.gz | prodigal -d GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/cds.fna -a GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:52:31,347] [INFO] Task succeeded: Prodigal
[2023-06-29 23:52:31,348] [INFO] Task started: HMMsearch
[2023-06-29 23:52:31,348] [INFO] Running command: hmmsearch --tblout GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference/reference_markers.hmm GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:52:31,546] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:52:31,548] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf083d16b-d774-47bc-85b6-e5c7d3c8adda/GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna.gz]
[2023-06-29 23:52:31,572] [INFO] Query marker FASTA was written to GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/markers.fasta
[2023-06-29 23:52:31,572] [INFO] Task started: Blastn
[2023-06-29 23:52:31,572] [INFO] Running command: blastn -query GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference/reference_markers.fasta -out GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:52:32,130] [INFO] Task succeeded: Blastn
[2023-06-29 23:52:32,137] [INFO] Selected 9 target genomes.
[2023-06-29 23:52:32,137] [INFO] Target genome list was writen to GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/target_genomes.txt
[2023-06-29 23:52:32,139] [INFO] Task started: fastANI
[2023-06-29 23:52:32,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgf083d16b-d774-47bc-85b6-e5c7d3c8adda/GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna.gz --refList GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/target_genomes.txt --output GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:52:39,528] [INFO] Task succeeded: fastANI
[2023-06-29 23:52:39,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:52:39,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:52:39,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:52:39,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 23:52:39,530] [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
--------------------------------------------------------------------------------
[2023-06-29 23:52:39,532] [INFO] DFAST Taxonomy check result was written to GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/tc_result.tsv
[2023-06-29 23:52:39,533] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:52:39,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:52:39,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference/checkm_data
[2023-06-29 23:52:39,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:52:39,561] [INFO] Task started: CheckM
[2023-06-29 23:52:39,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/checkm_input GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/checkm_result
[2023-06-29 23:53:01,439] [INFO] Task succeeded: CheckM
[2023-06-29 23:53:01,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:53:01,462] [INFO] ===== Completeness check finished =====
[2023-06-29 23:53:01,462] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:53:01,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/markers.fasta)
[2023-06-29 23:53:01,463] [INFO] Task started: Blastn
[2023-06-29 23:53:01,463] [INFO] Running command: blastn -query GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6f29b70-434b-4f4e-aaf8-2e68261f0d3e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:53:02,132] [INFO] Task succeeded: Blastn
[2023-06-29 23:53:02,136] [INFO] Selected 11 target genomes.
[2023-06-29 23:53:02,136] [INFO] Target genome list was writen to GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:53:02,141] [INFO] Task started: fastANI
[2023-06-29 23:53:02,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgf083d16b-d774-47bc-85b6-e5c7d3c8adda/GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna.gz --refList GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/target_genomes_gtdb.txt --output GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:53:07,414] [INFO] Task succeeded: fastANI
[2023-06-29 23:53:07,418] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:53:07,418] [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_003671065.1	s__QWPT01 sp003671065	97.1298	138	183	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	97.91	97.83	0.77	0.73	3	conclusive
GCA_003671025.1	s__QWPT01 sp003671025	78.8551	59	183	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.38	99.11	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-29 23:53:07,420] [INFO] GTDB search result was written to GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/result_gtdb.tsv
[2023-06-29 23:53:07,421] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:53:07,423] [INFO] DFAST_QC result json was written to GCA_903944245.1_freshwater_MAG_---_Loc090519-5m_bin-0620_genomic.fna/dqc_result.json
[2023-06-29 23:53:07,423] [INFO] DFAST_QC completed!
[2023-06-29 23:53:07,424] [INFO] Total running time: 0h0m42s