[2023-07-01 06:01:04,104] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:01:04,122] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:01:04,122] [INFO] DQC Reference Directory: /var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference
[2023-07-01 06:01:05,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:01:05,334] [INFO] Task started: Prodigal
[2023-07-01 06:01:05,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg981b283c-ef2b-458a-b085-81a24b359126/GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna.gz | prodigal -d GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/cds.fna -a GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:01:06,610] [INFO] Task succeeded: Prodigal
[2023-07-01 06:01:06,610] [INFO] Task started: HMMsearch
[2023-07-01 06:01:06,611] [INFO] Running command: hmmsearch --tblout GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference/reference_markers.hmm GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:01:06,902] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:01:06,904] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg981b283c-ef2b-458a-b085-81a24b359126/GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna.gz]
[2023-07-01 06:01:06,917] [INFO] Query marker FASTA was written to GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/markers.fasta
[2023-07-01 06:01:06,918] [INFO] Task started: Blastn
[2023-07-01 06:01:06,918] [INFO] Running command: blastn -query GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/markers.fasta -db /var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference/reference_markers.fasta -out GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:01:07,505] [INFO] Task succeeded: Blastn
[2023-07-01 06:01:07,509] [INFO] Selected 19 target genomes.
[2023-07-01 06:01:07,510] [INFO] Target genome list was writen to GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/target_genomes.txt
[2023-07-01 06:01:07,515] [INFO] Task started: fastANI
[2023-07-01 06:01:07,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg981b283c-ef2b-458a-b085-81a24b359126/GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna.gz --refList GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/target_genomes.txt --output GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:01:14,116] [INFO] Task succeeded: fastANI
[2023-07-01 06:01:14,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:01:14,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:01:14,119] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:01:14,120] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 06:01:14,120] [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 06:01:14,122] [INFO] DFAST Taxonomy check result was written to GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/tc_result.tsv
[2023-07-01 06:01:14,123] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:01:14,123] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:01:14,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference/checkm_data
[2023-07-01 06:01:14,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:01:14,140] [INFO] Task started: CheckM
[2023-07-01 06:01:14,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/checkm_input GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/checkm_result
[2023-07-01 06:01:26,167] [INFO] Task succeeded: CheckM
[2023-07-01 06:01:26,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 38.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:01:26,189] [INFO] ===== Completeness check finished =====
[2023-07-01 06:01:26,189] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:01:26,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/markers.fasta)
[2023-07-01 06:01:26,190] [INFO] Task started: Blastn
[2023-07-01 06:01:26,191] [INFO] Running command: blastn -query GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/markers.fasta -db /var/lib/cwl/stgf72cae72-7111-4a09-80e0-3a8bd368d101/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:01:26,918] [INFO] Task succeeded: Blastn
[2023-07-01 06:01:26,924] [INFO] Selected 13 target genomes.
[2023-07-01 06:01:26,924] [INFO] Target genome list was writen to GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:01:26,928] [INFO] Task started: fastANI
[2023-07-01 06:01:26,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg981b283c-ef2b-458a-b085-81a24b359126/GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna.gz --refList GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/target_genomes_gtdb.txt --output GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:01:29,005] [INFO] Task succeeded: fastANI
[2023-07-01 06:01:29,011] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:01:29,012] [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_003569185.1	s__Nanopelagicus sp003569185	92.0152	67	88	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287885.2	s__Nanopelagicus limnes	89.0641	83	88	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	80.7284	64	88	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
GCA_016870455.1	s__Nanopelagicus sp016870455	80.2975	59	88	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288005.1	s__Nanopelagicus hibericus	80.0758	63	88	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691185.1	s__Nanopelagicus sp009691185	79.3736	57	88	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:01:29,014] [INFO] GTDB search result was written to GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/result_gtdb.tsv
[2023-07-01 06:01:29,014] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:01:29,016] [INFO] DFAST_QC result json was written to GCA_903856375.1_freshwater_MAG_---_LaPlata-5m-a_bin-415_genomic.fna/dqc_result.json
[2023-07-01 06:01:29,016] [INFO] DFAST_QC completed!
[2023-07-01 06:01:29,017] [INFO] Total running time: 0h0m25s