[2023-07-01 04:21:50,753] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:21:50,755] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:21:50,755] [INFO] DQC Reference Directory: /var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference
[2023-07-01 04:21:52,063] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:21:52,064] [INFO] Task started: Prodigal
[2023-07-01 04:21:52,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg9363559e-2f11-4f8e-94d4-9bd5bf0eee80/GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna.gz | prodigal -d GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/cds.fna -a GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:21:55,422] [INFO] Task succeeded: Prodigal
[2023-07-01 04:21:55,423] [INFO] Task started: HMMsearch
[2023-07-01 04:21:55,423] [INFO] Running command: hmmsearch --tblout GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference/reference_markers.hmm GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:21:55,641] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:21:55,643] [INFO] Found 6/6 markers.
[2023-07-01 04:21:55,664] [INFO] Query marker FASTA was written to GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/markers.fasta
[2023-07-01 04:21:55,665] [INFO] Task started: Blastn
[2023-07-01 04:21:55,665] [INFO] Running command: blastn -query GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/markers.fasta -db /var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference/reference_markers.fasta -out GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:21:56,310] [INFO] Task succeeded: Blastn
[2023-07-01 04:21:56,315] [INFO] Selected 22 target genomes.
[2023-07-01 04:21:56,315] [INFO] Target genome list was writen to GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/target_genomes.txt
[2023-07-01 04:21:56,319] [INFO] Task started: fastANI
[2023-07-01 04:21:56,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg9363559e-2f11-4f8e-94d4-9bd5bf0eee80/GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna.gz --refList GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/target_genomes.txt --output GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:22:09,268] [INFO] Task succeeded: fastANI
[2023-07-01 04:22:09,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:22:09,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:22:09,272] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:22:09,272] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:22:09,272] [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 04:22:09,274] [INFO] DFAST Taxonomy check result was written to GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/tc_result.tsv
[2023-07-01 04:22:09,275] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:22:09,276] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:22:09,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference/checkm_data
[2023-07-01 04:22:09,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:22:09,302] [INFO] Task started: CheckM
[2023-07-01 04:22:09,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/checkm_input GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/checkm_result
[2023-07-01 04:22:27,426] [INFO] Task succeeded: CheckM
[2023-07-01 04:22:27,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:22:27,448] [INFO] ===== Completeness check finished =====
[2023-07-01 04:22:27,448] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:22:27,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/markers.fasta)
[2023-07-01 04:22:27,449] [INFO] Task started: Blastn
[2023-07-01 04:22:27,449] [INFO] Running command: blastn -query GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/markers.fasta -db /var/lib/cwl/stge0d57eeb-2c5b-4240-aa6d-afd91170e768/dqc_reference/reference_markers_gtdb.fasta -out GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:22:28,421] [INFO] Task succeeded: Blastn
[2023-07-01 04:22:28,426] [INFO] Selected 14 target genomes.
[2023-07-01 04:22:28,426] [INFO] Target genome list was writen to GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:22:28,428] [INFO] Task started: fastANI
[2023-07-01 04:22:28,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg9363559e-2f11-4f8e-94d4-9bd5bf0eee80/GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna.gz --refList GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/target_genomes_gtdb.txt --output GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:22:31,737] [INFO] Task succeeded: fastANI
[2023-07-01 04:22:31,745] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:22:31,745] [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_903825945.1	s__PALSA-747 sp903825945	99.8757	363	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.80	99.72	0.94	0.92	3	conclusive
GCA_903916775.1	s__PALSA-747 sp903916775	92.0045	229	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842855.1	s__PALSA-747 sp903842855	80.1782	56	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932695.1	s__PALSA-747 sp903932695	79.6515	130	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.67	98.37	0.76	0.73	5	-
GCA_903932705.1	s__PALSA-747 sp903932705	78.833	61	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897155.1	s__PALSA-747 sp903897155	78.29	59	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.95	98.34	0.84	0.73	51	-
GCA_903891755.1	s__PALSA-747 sp903891755	78.1379	71	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.94	98.90	0.76	0.73	3	-
GCA_903899375.1	s__PALSA-747 sp903899375	77.6645	58	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.46	99.00	0.86	0.79	59	-
GCA_903839355.1	s__PALSA-747 sp903839355	77.0784	50	401	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:22:31,747] [INFO] GTDB search result was written to GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/result_gtdb.tsv
[2023-07-01 04:22:31,748] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:22:31,751] [INFO] DFAST_QC result json was written to GCA_903834415.1_freshwater_MAG_---_MJ-time_bin-1573_genomic.fna/dqc_result.json
[2023-07-01 04:22:31,751] [INFO] DFAST_QC completed!
[2023-07-01 04:22:31,751] [INFO] Total running time: 0h0m41s