[2023-06-13 08:52:24,220] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:52:24,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:52:24,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference
[2023-06-13 08:52:25,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:52:25,490] [INFO] Task started: Prodigal
[2023-06-13 08:52:25,490] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa2b8c39-181a-46e5-bb5e-5ae3959cd14a/GCA_947450175.1_Jr-16oct17-294_genomic.fna.gz | prodigal -d GCA_947450175.1_Jr-16oct17-294_genomic.fna/cds.fna -a GCA_947450175.1_Jr-16oct17-294_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:28,199] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:28,200] [INFO] Task started: HMMsearch
[2023-06-13 08:52:28,200] [INFO] Running command: hmmsearch --tblout GCA_947450175.1_Jr-16oct17-294_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference/reference_markers.hmm GCA_947450175.1_Jr-16oct17-294_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:28,434] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:28,436] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa2b8c39-181a-46e5-bb5e-5ae3959cd14a/GCA_947450175.1_Jr-16oct17-294_genomic.fna.gz]
[2023-06-13 08:52:28,462] [INFO] Query marker FASTA was written to GCA_947450175.1_Jr-16oct17-294_genomic.fna/markers.fasta
[2023-06-13 08:52:28,462] [INFO] Task started: Blastn
[2023-06-13 08:52:28,462] [INFO] Running command: blastn -query GCA_947450175.1_Jr-16oct17-294_genomic.fna/markers.fasta -db /var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference/reference_markers.fasta -out GCA_947450175.1_Jr-16oct17-294_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:29,075] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:29,083] [INFO] Selected 25 target genomes.
[2023-06-13 08:52:29,083] [INFO] Target genome list was writen to GCA_947450175.1_Jr-16oct17-294_genomic.fna/target_genomes.txt
[2023-06-13 08:52:29,116] [INFO] Task started: fastANI
[2023-06-13 08:52:29,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa2b8c39-181a-46e5-bb5e-5ae3959cd14a/GCA_947450175.1_Jr-16oct17-294_genomic.fna.gz --refList GCA_947450175.1_Jr-16oct17-294_genomic.fna/target_genomes.txt --output GCA_947450175.1_Jr-16oct17-294_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:40,748] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:40,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:40,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:40,751] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:52:40,751] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 08:52:40,752] [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
--------------------------------------------------------------------------------
[2023-06-13 08:52:40,754] [INFO] DFAST Taxonomy check result was written to GCA_947450175.1_Jr-16oct17-294_genomic.fna/tc_result.tsv
[2023-06-13 08:52:40,755] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:40,755] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:40,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference/checkm_data
[2023-06-13 08:52:40,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:40,783] [INFO] Task started: CheckM
[2023-06-13 08:52:40,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947450175.1_Jr-16oct17-294_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947450175.1_Jr-16oct17-294_genomic.fna/checkm_input GCA_947450175.1_Jr-16oct17-294_genomic.fna/checkm_result
[2023-06-13 08:52:57,403] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:57,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:57,430] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:57,430] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:57,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947450175.1_Jr-16oct17-294_genomic.fna/markers.fasta)
[2023-06-13 08:52:57,434] [INFO] Task started: Blastn
[2023-06-13 08:52:57,434] [INFO] Running command: blastn -query GCA_947450175.1_Jr-16oct17-294_genomic.fna/markers.fasta -db /var/lib/cwl/stgee6a196b-9d2f-4cc2-870c-2fa8df680406/dqc_reference/reference_markers_gtdb.fasta -out GCA_947450175.1_Jr-16oct17-294_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:58,335] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:58,340] [INFO] Selected 12 target genomes.
[2023-06-13 08:52:58,340] [INFO] Target genome list was writen to GCA_947450175.1_Jr-16oct17-294_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:58,347] [INFO] Task started: fastANI
[2023-06-13 08:52:58,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa2b8c39-181a-46e5-bb5e-5ae3959cd14a/GCA_947450175.1_Jr-16oct17-294_genomic.fna.gz --refList GCA_947450175.1_Jr-16oct17-294_genomic.fna/target_genomes_gtdb.txt --output GCA_947450175.1_Jr-16oct17-294_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:53:01,448] [INFO] Task succeeded: fastANI
[2023-06-13 08:53:01,462] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:53:01,462] [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_009698445.1	s__Planktophila sp009698445	90.0392	285	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.86	99.84	0.93	0.93	3	-
GCA_009726135.1	s__Planktophila sp009726135	86.8869	271	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.91	99.82	0.93	0.91	6	-
GCF_002288185.1	s__Planktophila vernalis	82.4939	262	370	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	82.4619	276	370	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	82.2847	256	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	96.66	96.52	0.78	0.69	3	-
GCA_003569265.1	s__Planktophila sp003569265	81.919	127	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.55	99.55	0.94	0.94	2	-
GCA_903904665.1	s__Planktophila sp903904665	81.5052	216	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.61	99.61	0.91	0.91	2	-
GCA_018969355.1	s__Planktophila sp018969355	81.4283	229	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918325.1	s__Planktophila sp903918325	81.4077	179	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	98.89	98.77	0.80	0.78	4	-
GCA_903894425.1	s__Planktophila sp903894425	81.2195	214	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705165.1	s__Planktophila sp009705165	80.6838	142	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825015.1	s__Planktophila sp903825015	80.616	206	370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	99.76	99.71	0.87	0.84	4	-
--------------------------------------------------------------------------------
[2023-06-13 08:53:01,464] [INFO] GTDB search result was written to GCA_947450175.1_Jr-16oct17-294_genomic.fna/result_gtdb.tsv
[2023-06-13 08:53:01,465] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:53:01,468] [INFO] DFAST_QC result json was written to GCA_947450175.1_Jr-16oct17-294_genomic.fna/dqc_result.json
[2023-06-13 08:53:01,468] [INFO] DFAST_QC completed!
[2023-06-13 08:53:01,468] [INFO] Total running time: 0h0m37s