[2023-06-19 05:25:05,265] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:25:05,270] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:25:05,270] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference
[2023-06-19 05:25:07,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:25:07,576] [INFO] Task started: Prodigal
[2023-06-19 05:25:07,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a0c37a2-939a-430f-9123-92fdd85b3ae7/GCA_018969355.1_ASM1896935v1_genomic.fna.gz | prodigal -d GCA_018969355.1_ASM1896935v1_genomic.fna/cds.fna -a GCA_018969355.1_ASM1896935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:25:10,942] [INFO] Task succeeded: Prodigal
[2023-06-19 05:25:10,942] [INFO] Task started: HMMsearch
[2023-06-19 05:25:10,942] [INFO] Running command: hmmsearch --tblout GCA_018969355.1_ASM1896935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference/reference_markers.hmm GCA_018969355.1_ASM1896935v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:25:11,168] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:25:11,170] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a0c37a2-939a-430f-9123-92fdd85b3ae7/GCA_018969355.1_ASM1896935v1_genomic.fna.gz]
[2023-06-19 05:25:11,193] [INFO] Query marker FASTA was written to GCA_018969355.1_ASM1896935v1_genomic.fna/markers.fasta
[2023-06-19 05:25:11,193] [INFO] Task started: Blastn
[2023-06-19 05:25:11,193] [INFO] Running command: blastn -query GCA_018969355.1_ASM1896935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference/reference_markers.fasta -out GCA_018969355.1_ASM1896935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:12,865] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:12,870] [INFO] Selected 25 target genomes.
[2023-06-19 05:25:12,871] [INFO] Target genome list was writen to GCA_018969355.1_ASM1896935v1_genomic.fna/target_genomes.txt
[2023-06-19 05:25:12,874] [INFO] Task started: fastANI
[2023-06-19 05:25:12,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a0c37a2-939a-430f-9123-92fdd85b3ae7/GCA_018969355.1_ASM1896935v1_genomic.fna.gz --refList GCA_018969355.1_ASM1896935v1_genomic.fna/target_genomes.txt --output GCA_018969355.1_ASM1896935v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:23,285] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:23,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:23,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:23,288] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:23,288] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:25:23,288] [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
--------------------------------------------------------------------------------
[2023-06-19 05:25:23,290] [INFO] DFAST Taxonomy check result was written to GCA_018969355.1_ASM1896935v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:23,292] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:23,292] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:23,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference/checkm_data
[2023-06-19 05:25:23,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:23,316] [INFO] Task started: CheckM
[2023-06-19 05:25:23,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018969355.1_ASM1896935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018969355.1_ASM1896935v1_genomic.fna/checkm_input GCA_018969355.1_ASM1896935v1_genomic.fna/checkm_result
[2023-06-19 05:25:41,019] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:41,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:41,056] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:41,057] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:41,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018969355.1_ASM1896935v1_genomic.fna/markers.fasta)
[2023-06-19 05:25:41,057] [INFO] Task started: Blastn
[2023-06-19 05:25:41,057] [INFO] Running command: blastn -query GCA_018969355.1_ASM1896935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0bdb278-8ce8-4f1c-8678-5e020429592a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018969355.1_ASM1896935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:41,963] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:41,969] [INFO] Selected 7 target genomes.
[2023-06-19 05:25:41,969] [INFO] Target genome list was writen to GCA_018969355.1_ASM1896935v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:42,000] [INFO] Task started: fastANI
[2023-06-19 05:25:42,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a0c37a2-939a-430f-9123-92fdd85b3ae7/GCA_018969355.1_ASM1896935v1_genomic.fna.gz --refList GCA_018969355.1_ASM1896935v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018969355.1_ASM1896935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:25:44,243] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:44,253] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:25:44,253] [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_018969355.1	s__Planktophila sp018969355	100.0	421	423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002284895.1	s__Planktophila sp002284895	87.145	375	423	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	86.9875	351	423	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	86.2242	316	423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_010024385.1	s__Planktophila sp010024385	86.1512	334	423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.43	99.35	0.91	0.87	13	-
GCA_005789205.1	s__Planktophila sp005789205	85.9562	257	423	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	84.6481	177	423	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.55	99.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:25:44,257] [INFO] GTDB search result was written to GCA_018969355.1_ASM1896935v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:25:44,258] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:25:44,263] [INFO] DFAST_QC result json was written to GCA_018969355.1_ASM1896935v1_genomic.fna/dqc_result.json
[2023-06-19 05:25:44,264] [INFO] DFAST_QC completed!
[2023-06-19 05:25:44,264] [INFO] Total running time: 0h0m39s