[2023-06-30 12:52:57,445] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:52:57,447] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:52:57,447] [INFO] DQC Reference Directory: /var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference
[2023-06-30 12:52:58,876] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:52:58,877] [INFO] Task started: Prodigal
[2023-06-30 12:52:58,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgab9a195a-3443-4883-92d3-0be096f8b21b/GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna.gz | prodigal -d GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/cds.fna -a GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:53:00,043] [INFO] Task succeeded: Prodigal
[2023-06-30 12:53:00,044] [INFO] Task started: HMMsearch
[2023-06-30 12:53:00,044] [INFO] Running command: hmmsearch --tblout GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference/reference_markers.hmm GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:53:00,214] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:53:00,215] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgab9a195a-3443-4883-92d3-0be096f8b21b/GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna.gz]
[2023-06-30 12:53:00,231] [INFO] Query marker FASTA was written to GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/markers.fasta
[2023-06-30 12:53:00,232] [INFO] Task started: Blastn
[2023-06-30 12:53:00,232] [INFO] Running command: blastn -query GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference/reference_markers.fasta -out GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:53:00,752] [INFO] Task succeeded: Blastn
[2023-06-30 12:53:00,755] [INFO] Selected 2 target genomes.
[2023-06-30 12:53:00,756] [INFO] Target genome list was writen to GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-30 12:53:00,758] [INFO] Task started: fastANI
[2023-06-30 12:53:00,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgab9a195a-3443-4883-92d3-0be096f8b21b/GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna.gz --refList GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:53:01,856] [INFO] Task succeeded: fastANI
[2023-06-30 12:53:01,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:53:01,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:53:01,858] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:53:01,858] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:53:01,858] [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 12:53:01,860] [INFO] DFAST Taxonomy check result was written to GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-30 12:53:01,860] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:53:01,861] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:53:01,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference/checkm_data
[2023-06-30 12:53:01,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:53:01,876] [INFO] Task started: CheckM
[2023-06-30 12:53:01,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/checkm_input GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/checkm_result
[2023-06-30 12:53:14,071] [INFO] Task succeeded: CheckM
[2023-06-30 12:53:14,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:53:14,092] [INFO] ===== Completeness check finished =====
[2023-06-30 12:53:14,092] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:53:14,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/markers.fasta)
[2023-06-30 12:53:14,093] [INFO] Task started: Blastn
[2023-06-30 12:53:14,094] [INFO] Running command: blastn -query GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stge6b3c670-8762-4dd9-9b8b-f26f1db1dcc8/dqc_reference/reference_markers_gtdb.fasta -out GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:53:14,671] [INFO] Task succeeded: Blastn
[2023-06-30 12:53:14,677] [INFO] Selected 6 target genomes.
[2023-06-30 12:53:14,677] [INFO] Target genome list was writen to GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:53:14,685] [INFO] Task started: fastANI
[2023-06-30 12:53:14,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgab9a195a-3443-4883-92d3-0be096f8b21b/GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna.gz --refList GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:53:15,838] [INFO] Task succeeded: fastANI
[2023-06-30 12:53:15,844] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:53:15,845] [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_014384285.1	s__Actinomarina sp014384285	99.0003	203	210	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	conclusive
GCA_002308095.1	s__Actinomarina sp002308095	81.318	114	210	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510965.1	s__Actinomarina sp002683085	80.7141	100	210	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_014239265.1	s__Actinomarina sp014239265	80.1904	132	210	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169845.1	s__Actinomarina sp002169845	80.0998	83	210	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:53:15,847] [INFO] GTDB search result was written to GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-30 12:53:15,847] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:53:15,850] [INFO] DFAST_QC result json was written to GCA_943841115.1_20200310_Bin_contigs_Bin_623_1-contigs.fa_genomic.fna/dqc_result.json
[2023-06-30 12:53:15,850] [INFO] DFAST_QC completed!
[2023-06-30 12:53:15,850] [INFO] Total running time: 0h0m18s