[2023-06-30 03:57:01,314] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:57:01,317] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:57:01,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference
[2023-06-30 03:57:03,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:57:03,400] [INFO] Task started: Prodigal
[2023-06-30 03:57:03,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b14e15d-985d-498c-bf2b-8c0668fbba90/GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna.gz | prodigal -d GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/cds.fna -a GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:57:05,210] [INFO] Task succeeded: Prodigal
[2023-06-30 03:57:05,210] [INFO] Task started: HMMsearch
[2023-06-30 03:57:05,210] [INFO] Running command: hmmsearch --tblout GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference/reference_markers.hmm GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:57:05,471] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:57:05,472] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b14e15d-985d-498c-bf2b-8c0668fbba90/GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna.gz]
[2023-06-30 03:57:05,492] [INFO] Query marker FASTA was written to GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/markers.fasta
[2023-06-30 03:57:05,492] [INFO] Task started: Blastn
[2023-06-30 03:57:05,492] [INFO] Running command: blastn -query GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/markers.fasta -db /var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference/reference_markers.fasta -out GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:57:08,432] [INFO] Task succeeded: Blastn
[2023-06-30 03:57:08,443] [INFO] Selected 26 target genomes.
[2023-06-30 03:57:08,443] [INFO] Target genome list was writen to GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/target_genomes.txt
[2023-06-30 03:57:08,449] [INFO] Task started: fastANI
[2023-06-30 03:57:08,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b14e15d-985d-498c-bf2b-8c0668fbba90/GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna.gz --refList GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/target_genomes.txt --output GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:57:21,639] [INFO] Task succeeded: fastANI
[2023-06-30 03:57:21,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:57:21,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:57:21,643] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:57:21,643] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 03:57:21,643] [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 03:57:21,646] [INFO] DFAST Taxonomy check result was written to GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/tc_result.tsv
[2023-06-30 03:57:21,646] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:57:21,647] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:57:21,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference/checkm_data
[2023-06-30 03:57:21,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:57:21,668] [INFO] Task started: CheckM
[2023-06-30 03:57:21,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/checkm_input GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/checkm_result
[2023-06-30 03:57:35,477] [INFO] Task succeeded: CheckM
[2023-06-30 03:57:35,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:57:35,502] [INFO] ===== Completeness check finished =====
[2023-06-30 03:57:35,503] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:57:35,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/markers.fasta)
[2023-06-30 03:57:35,504] [INFO] Task started: Blastn
[2023-06-30 03:57:35,504] [INFO] Running command: blastn -query GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/markers.fasta -db /var/lib/cwl/stg05604d28-a8ba-470c-9568-1a752d8b1d4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:57:36,409] [INFO] Task succeeded: Blastn
[2023-06-30 03:57:36,414] [INFO] Selected 10 target genomes.
[2023-06-30 03:57:36,414] [INFO] Target genome list was writen to GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:57:36,420] [INFO] Task started: fastANI
[2023-06-30 03:57:36,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b14e15d-985d-498c-bf2b-8c0668fbba90/GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna.gz --refList GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/target_genomes_gtdb.txt --output GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:57:38,292] [INFO] Task succeeded: fastANI
[2023-06-30 03:57:38,309] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 03:57:38,310] [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
GCF_002288225.1	s__Planktophila dulcis	90.4135	109	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	97.64	97.42	0.94	0.93	3	-
GCA_009701945.1	s__Planktophila sp009701945	89.8244	81	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.37	98.37	0.73	0.73	2	-
GCA_002284855.1	s__Planktophila sp002284855	83.864	97	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002288065.1	s__Planktophila sulfonica	83.6142	95	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701085.1	s__Planktophila sp009701085	83.0326	58	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.29	98.29	0.74	0.74	2	-
GCA_000372185.1	s__Planktophila sp000372185	82.9275	72	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865885.1	s__Planktophila sp903865885	82.6575	63	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845465.1	s__Planktophila sp903845465	81.4661	74	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.37	98.68	0.87	0.84	5	-
GCA_009700365.1	s__Planktophila sp009700365	79.9352	59	119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.64	98.64	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-30 03:57:38,312] [INFO] GTDB search result was written to GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/result_gtdb.tsv
[2023-06-30 03:57:38,313] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:57:38,317] [INFO] DFAST_QC result json was written to GCA_903856795.1_freshwater_MAG_---_Ja2-D2_bin-0504_genomic.fna/dqc_result.json
[2023-06-30 03:57:38,317] [INFO] DFAST_QC completed!
[2023-06-30 03:57:38,318] [INFO] Total running time: 0h0m37s