[2023-06-17 04:57:19,195] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:57:19,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:57:19,199] [INFO] DQC Reference Directory: /var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference
[2023-06-17 04:57:20,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:57:20,551] [INFO] Task started: Prodigal
[2023-06-17 04:57:20,551] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf32d714-445c-43fc-9fdb-79b6d52cbb12/GCA_905182685.1_FRAM18_bin086_genomic.fna.gz | prodigal -d GCA_905182685.1_FRAM18_bin086_genomic.fna/cds.fna -a GCA_905182685.1_FRAM18_bin086_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:57:22,916] [INFO] Task succeeded: Prodigal
[2023-06-17 04:57:22,916] [INFO] Task started: HMMsearch
[2023-06-17 04:57:22,916] [INFO] Running command: hmmsearch --tblout GCA_905182685.1_FRAM18_bin086_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference/reference_markers.hmm GCA_905182685.1_FRAM18_bin086_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:57:23,128] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:57:23,130] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbf32d714-445c-43fc-9fdb-79b6d52cbb12/GCA_905182685.1_FRAM18_bin086_genomic.fna.gz]
[2023-06-17 04:57:23,161] [INFO] Query marker FASTA was written to GCA_905182685.1_FRAM18_bin086_genomic.fna/markers.fasta
[2023-06-17 04:57:23,161] [INFO] Task started: Blastn
[2023-06-17 04:57:23,162] [INFO] Running command: blastn -query GCA_905182685.1_FRAM18_bin086_genomic.fna/markers.fasta -db /var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference/reference_markers.fasta -out GCA_905182685.1_FRAM18_bin086_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:23,700] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:23,704] [INFO] Selected 13 target genomes.
[2023-06-17 04:57:23,704] [INFO] Target genome list was writen to GCA_905182685.1_FRAM18_bin086_genomic.fna/target_genomes.txt
[2023-06-17 04:57:23,717] [INFO] Task started: fastANI
[2023-06-17 04:57:23,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf32d714-445c-43fc-9fdb-79b6d52cbb12/GCA_905182685.1_FRAM18_bin086_genomic.fna.gz --refList GCA_905182685.1_FRAM18_bin086_genomic.fna/target_genomes.txt --output GCA_905182685.1_FRAM18_bin086_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:57:29,395] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:29,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:57:29,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:57:29,399] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:57:29,399] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 04:57:29,399] [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
--------------------------------------------------------------------------------
[2023-06-17 04:57:29,402] [INFO] DFAST Taxonomy check result was written to GCA_905182685.1_FRAM18_bin086_genomic.fna/tc_result.tsv
[2023-06-17 04:57:29,403] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:57:29,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:57:29,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference/checkm_data
[2023-06-17 04:57:29,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:57:29,426] [INFO] Task started: CheckM
[2023-06-17 04:57:29,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905182685.1_FRAM18_bin086_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905182685.1_FRAM18_bin086_genomic.fna/checkm_input GCA_905182685.1_FRAM18_bin086_genomic.fna/checkm_result
[2023-06-17 04:57:44,550] [INFO] Task succeeded: CheckM
[2023-06-17 04:57:44,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:57:44,572] [INFO] ===== Completeness check finished =====
[2023-06-17 04:57:44,572] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:57:44,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905182685.1_FRAM18_bin086_genomic.fna/markers.fasta)
[2023-06-17 04:57:44,573] [INFO] Task started: Blastn
[2023-06-17 04:57:44,573] [INFO] Running command: blastn -query GCA_905182685.1_FRAM18_bin086_genomic.fna/markers.fasta -db /var/lib/cwl/stge0c4f1e7-7231-447c-8b1a-40841a613fee/dqc_reference/reference_markers_gtdb.fasta -out GCA_905182685.1_FRAM18_bin086_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:45,066] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:45,070] [INFO] Selected 8 target genomes.
[2023-06-17 04:57:45,070] [INFO] Target genome list was writen to GCA_905182685.1_FRAM18_bin086_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:57:45,079] [INFO] Task started: fastANI
[2023-06-17 04:57:45,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf32d714-445c-43fc-9fdb-79b6d52cbb12/GCA_905182685.1_FRAM18_bin086_genomic.fna.gz --refList GCA_905182685.1_FRAM18_bin086_genomic.fna/target_genomes_gtdb.txt --output GCA_905182685.1_FRAM18_bin086_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:57:48,578] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:48,588] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 04:57:48,588] [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_000153745.1	s__Amylibacter sp000153745	98.3987	350	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	98.38	97.19	0.95	0.89	11	conclusive
GCA_900197625.1	s__Amylibacter sp900197625	84.5543	279	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.40	99.20	0.94	0.94	3	-
GCA_905182285.1	s__Amylibacter sp905182285	81.6355	253	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.59	99.59	0.86	0.86	2	-
GCA_905181935.1	s__Amylibacter sp905181935	78.985	128	366	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 04:57:48,590] [INFO] GTDB search result was written to GCA_905182685.1_FRAM18_bin086_genomic.fna/result_gtdb.tsv
[2023-06-17 04:57:48,590] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:57:48,593] [INFO] DFAST_QC result json was written to GCA_905182685.1_FRAM18_bin086_genomic.fna/dqc_result.json
[2023-06-17 04:57:48,593] [INFO] DFAST_QC completed!
[2023-06-17 04:57:48,593] [INFO] Total running time: 0h0m29s