[2023-06-30 02:29:47,125] [INFO] DFAST_QC pipeline started.
[2023-06-30 02:29:47,130] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 02:29:47,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference
[2023-06-30 02:29:49,147] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 02:29:49,148] [INFO] Task started: Prodigal
[2023-06-30 02:29:49,148] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e6d50c-5979-4118-a236-53a686bc223a/GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna.gz | prodigal -d GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/cds.fna -a GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 02:29:51,937] [INFO] Task succeeded: Prodigal
[2023-06-30 02:29:51,937] [INFO] Task started: HMMsearch
[2023-06-30 02:29:51,938] [INFO] Running command: hmmsearch --tblout GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference/reference_markers.hmm GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/protein.faa > /dev/null
[2023-06-30 02:29:52,156] [INFO] Task succeeded: HMMsearch
[2023-06-30 02:29:52,158] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40e6d50c-5979-4118-a236-53a686bc223a/GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna.gz]
[2023-06-30 02:29:52,177] [INFO] Query marker FASTA was written to GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/markers.fasta
[2023-06-30 02:29:52,178] [INFO] Task started: Blastn
[2023-06-30 02:29:52,178] [INFO] Running command: blastn -query GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/markers.fasta -db /var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference/reference_markers.fasta -out GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:29:52,906] [INFO] Task succeeded: Blastn
[2023-06-30 02:29:52,911] [INFO] Selected 19 target genomes.
[2023-06-30 02:29:52,911] [INFO] Target genome list was writen to GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/target_genomes.txt
[2023-06-30 02:29:52,916] [INFO] Task started: fastANI
[2023-06-30 02:29:52,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e6d50c-5979-4118-a236-53a686bc223a/GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna.gz --refList GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/target_genomes.txt --output GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 02:30:00,045] [INFO] Task succeeded: fastANI
[2023-06-30 02:30:00,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 02:30:00,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 02:30:00,049] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 02:30:00,049] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 02:30:00,049] [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 02:30:00,052] [INFO] DFAST Taxonomy check result was written to GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/tc_result.tsv
[2023-06-30 02:30:00,052] [INFO] ===== Taxonomy check completed =====
[2023-06-30 02:30:00,053] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 02:30:00,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference/checkm_data
[2023-06-30 02:30:00,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 02:30:00,077] [INFO] Task started: CheckM
[2023-06-30 02:30:00,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/checkm_input GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/checkm_result
[2023-06-30 02:30:16,588] [INFO] Task succeeded: CheckM
[2023-06-30 02:30:16,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 02:30:16,614] [INFO] ===== Completeness check finished =====
[2023-06-30 02:30:16,614] [INFO] ===== Start GTDB Search =====
[2023-06-30 02:30:16,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/markers.fasta)
[2023-06-30 02:30:16,615] [INFO] Task started: Blastn
[2023-06-30 02:30:16,615] [INFO] Running command: blastn -query GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/markers.fasta -db /var/lib/cwl/stg5129af29-c703-4818-b493-9f5c97d4e8c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:30:17,407] [INFO] Task succeeded: Blastn
[2023-06-30 02:30:17,412] [INFO] Selected 14 target genomes.
[2023-06-30 02:30:17,412] [INFO] Target genome list was writen to GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 02:30:17,417] [INFO] Task started: fastANI
[2023-06-30 02:30:17,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e6d50c-5979-4118-a236-53a686bc223a/GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna.gz --refList GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/target_genomes_gtdb.txt --output GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 02:30:20,288] [INFO] Task succeeded: fastANI
[2023-06-30 02:30:20,299] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 02:30:20,299] [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_903898555.1	s__PALSA-747 sp903898555	99.3888	225	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	97.88	96.14	0.83	0.71	18	conclusive
GCA_903827945.1	s__PALSA-747 sp903827945	80.9185	163	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.47	99.25	0.93	0.89	10	-
GCA_903852585.1	s__PALSA-747 sp903852585	80.0454	97	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.67	99.56	0.92	0.91	12	-
GCA_903844115.1	s__PALSA-747 sp903844115	78.9261	87	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.13	98.59	0.83	0.78	5	-
GCA_903907665.1	s__PALSA-747 sp903907665	78.7144	85	268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.11	99.10	0.80	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-30 02:30:20,301] [INFO] GTDB search result was written to GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/result_gtdb.tsv
[2023-06-30 02:30:20,302] [INFO] ===== GTDB Search completed =====
[2023-06-30 02:30:20,304] [INFO] DFAST_QC result json was written to GCA_903853665.1_freshwater_MAG_---_MJ-time_bin-6296_genomic.fna/dqc_result.json
[2023-06-30 02:30:20,304] [INFO] DFAST_QC completed!
[2023-06-30 02:30:20,304] [INFO] Total running time: 0h0m33s