[2023-06-05 10:53:16,799] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:53:16,802] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:53:16,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference
[2023-06-05 10:53:19,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:53:19,113] [INFO] Task started: Prodigal
[2023-06-05 10:53:19,113] [INFO] Running command: gunzip -c /var/lib/cwl/stg983d4ba9-40ac-42d2-92e8-7cf537c26d23/GCA_010032005.1_ASM1003200v1_genomic.fna.gz | prodigal -d GCA_010032005.1_ASM1003200v1_genomic.fna/cds.fna -a GCA_010032005.1_ASM1003200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:53:21,996] [INFO] Task succeeded: Prodigal
[2023-06-05 10:53:21,996] [INFO] Task started: HMMsearch
[2023-06-05 10:53:21,997] [INFO] Running command: hmmsearch --tblout GCA_010032005.1_ASM1003200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference/reference_markers.hmm GCA_010032005.1_ASM1003200v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:53:22,216] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:53:22,218] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg983d4ba9-40ac-42d2-92e8-7cf537c26d23/GCA_010032005.1_ASM1003200v1_genomic.fna.gz]
[2023-06-05 10:53:22,240] [INFO] Query marker FASTA was written to GCA_010032005.1_ASM1003200v1_genomic.fna/markers.fasta
[2023-06-05 10:53:22,240] [INFO] Task started: Blastn
[2023-06-05 10:53:22,241] [INFO] Running command: blastn -query GCA_010032005.1_ASM1003200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference/reference_markers.fasta -out GCA_010032005.1_ASM1003200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:53:23,444] [INFO] Task succeeded: Blastn
[2023-06-05 10:53:23,448] [INFO] Selected 21 target genomes.
[2023-06-05 10:53:23,449] [INFO] Target genome list was writen to GCA_010032005.1_ASM1003200v1_genomic.fna/target_genomes.txt
[2023-06-05 10:53:23,593] [INFO] Task started: fastANI
[2023-06-05 10:53:23,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg983d4ba9-40ac-42d2-92e8-7cf537c26d23/GCA_010032005.1_ASM1003200v1_genomic.fna.gz --refList GCA_010032005.1_ASM1003200v1_genomic.fna/target_genomes.txt --output GCA_010032005.1_ASM1003200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:53:31,690] [INFO] Task succeeded: fastANI
[2023-06-05 10:53:31,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:53:31,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:53:31,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:53:31,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 10:53:31,693] [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
--------------------------------------------------------------------------------
[2023-06-05 10:53:31,695] [INFO] DFAST Taxonomy check result was written to GCA_010032005.1_ASM1003200v1_genomic.fna/tc_result.tsv
[2023-06-05 10:53:31,696] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:53:31,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:53:31,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference/checkm_data
[2023-06-05 10:53:31,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:53:31,719] [INFO] Task started: CheckM
[2023-06-05 10:53:31,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010032005.1_ASM1003200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010032005.1_ASM1003200v1_genomic.fna/checkm_input GCA_010032005.1_ASM1003200v1_genomic.fna/checkm_result
[2023-06-05 10:53:50,005] [INFO] Task succeeded: CheckM
[2023-06-05 10:53:50,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.06%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:53:50,025] [INFO] ===== Completeness check finished =====
[2023-06-05 10:53:50,025] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:53:50,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010032005.1_ASM1003200v1_genomic.fna/markers.fasta)
[2023-06-05 10:53:50,026] [INFO] Task started: Blastn
[2023-06-05 10:53:50,026] [INFO] Running command: blastn -query GCA_010032005.1_ASM1003200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6da612e8-7aba-458f-907d-018f3deb476a/dqc_reference/reference_markers_gtdb.fasta -out GCA_010032005.1_ASM1003200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:53:50,854] [INFO] Task succeeded: Blastn
[2023-06-05 10:53:50,858] [INFO] Selected 7 target genomes.
[2023-06-05 10:53:50,858] [INFO] Target genome list was writen to GCA_010032005.1_ASM1003200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:53:50,863] [INFO] Task started: fastANI
[2023-06-05 10:53:50,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg983d4ba9-40ac-42d2-92e8-7cf537c26d23/GCA_010032005.1_ASM1003200v1_genomic.fna.gz --refList GCA_010032005.1_ASM1003200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010032005.1_ASM1003200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:53:52,872] [INFO] Task succeeded: fastANI
[2023-06-05 10:53:52,887] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:53:52,887] [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_010024385.1	s__Planktophila sp010024385	99.4225	329	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.43	99.35	0.91	0.87	13	conclusive
GCA_005789205.1	s__Planktophila sp005789205	93.9579	245	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288185.1	s__Planktophila vernalis	91.1823	336	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002284895.1	s__Planktophila sp002284895	89.2352	328	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378885.1	s__Planktophila sp000378885	87.3432	284	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_018969355.1	s__Planktophila sp018969355	86.186	290	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569265.1	s__Planktophila sp003569265	86.0147	173	368	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.55	99.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-05 10:53:52,890] [INFO] GTDB search result was written to GCA_010032005.1_ASM1003200v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:53:52,890] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:53:52,893] [INFO] DFAST_QC result json was written to GCA_010032005.1_ASM1003200v1_genomic.fna/dqc_result.json
[2023-06-05 10:53:52,893] [INFO] DFAST_QC completed!
[2023-06-05 10:53:52,893] [INFO] Total running time: 0h0m36s