[2023-06-30 13:16:07,469] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:16:07,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:16:07,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference
[2023-06-30 13:16:08,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:16:08,709] [INFO] Task started: Prodigal
[2023-06-30 13:16:08,709] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3e899c7-bdde-492a-ab6d-27563d78e21f/GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna.gz | prodigal -d GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/cds.fna -a GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:16:30,954] [INFO] Task succeeded: Prodigal
[2023-06-30 13:16:30,955] [INFO] Task started: HMMsearch
[2023-06-30 13:16:30,955] [INFO] Running command: hmmsearch --tblout GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference/reference_markers.hmm GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:16:31,203] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:16:31,205] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb3e899c7-bdde-492a-ab6d-27563d78e21f/GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna.gz]
[2023-06-30 13:16:31,243] [INFO] Query marker FASTA was written to GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/markers.fasta
[2023-06-30 13:16:31,244] [INFO] Task started: Blastn
[2023-06-30 13:16:31,244] [INFO] Running command: blastn -query GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference/reference_markers.fasta -out GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:16:31,742] [INFO] Task succeeded: Blastn
[2023-06-30 13:16:31,746] [INFO] Selected 7 target genomes.
[2023-06-30 13:16:31,746] [INFO] Target genome list was writen to GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/target_genomes.txt
[2023-06-30 13:16:31,748] [INFO] Task started: fastANI
[2023-06-30 13:16:31,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e899c7-bdde-492a-ab6d-27563d78e21f/GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna.gz --refList GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/target_genomes.txt --output GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:16:35,609] [INFO] Task succeeded: fastANI
[2023-06-30 13:16:35,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:16:35,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:16:35,612] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:16:35,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:16:35,613] [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
--------------------------------------------------------------------------------
[2023-06-30 13:16:35,615] [INFO] DFAST Taxonomy check result was written to GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/tc_result.tsv
[2023-06-30 13:16:35,616] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:16:35,616] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:16:35,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference/checkm_data
[2023-06-30 13:16:35,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:16:35,661] [INFO] Task started: CheckM
[2023-06-30 13:16:35,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/checkm_input GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/checkm_result
[2023-06-30 13:17:37,516] [INFO] Task succeeded: CheckM
[2023-06-30 13:17:37,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:17:37,539] [INFO] ===== Completeness check finished =====
[2023-06-30 13:17:37,539] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:17:37,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/markers.fasta)
[2023-06-30 13:17:37,540] [INFO] Task started: Blastn
[2023-06-30 13:17:37,540] [INFO] Running command: blastn -query GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d2707a9-6f59-498e-8a1a-7e8a91ade85e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:17:38,042] [INFO] Task succeeded: Blastn
[2023-06-30 13:17:38,047] [INFO] Selected 9 target genomes.
[2023-06-30 13:17:38,047] [INFO] Target genome list was writen to GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:17:38,050] [INFO] Task started: fastANI
[2023-06-30 13:17:38,050] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e899c7-bdde-492a-ab6d-27563d78e21f/GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna.gz --refList GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/target_genomes_gtdb.txt --output GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:17:44,867] [INFO] Task succeeded: fastANI
[2023-06-30 13:17:44,882] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:17:44,882] [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_903884535.1	s__UBA11358 sp903884535	99.1606	557	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.82	0.93	0.89	5	conclusive
GCA_903850425.1	s__UBA11358 sp903850425	80.4578	357	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944085.1	s__UBA11358 sp903944085	79.8894	306	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_003455565.1	s__UBA11358 sp003455565	79.6611	209	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903833055.1	s__UBA11358 sp903833055	79.1057	205	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.65	99.64	0.85	0.82	3	-
GCA_903921455.1	s__UBA11358 sp903921455	78.5306	226	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878805.1	s__UBA11358 sp903878805	78.4902	172	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.90	0.92	0.92	2	-
GCA_903858275.1	s__UBA11358 sp903858275	78.2592	158	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.00	98.19	0.88	0.83	3	-
GCA_903842235.1	s__UBA11358 sp903842235	77.6801	154	748	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:17:44,884] [INFO] GTDB search result was written to GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/result_gtdb.tsv
[2023-06-30 13:17:44,885] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:17:44,888] [INFO] DFAST_QC result json was written to GCA_903898375.1_freshwater_MAG_---_AM3_bin-1191_genomic.fna/dqc_result.json
[2023-06-30 13:17:44,888] [INFO] DFAST_QC completed!
[2023-06-30 13:17:44,888] [INFO] Total running time: 0h1m37s