[2023-06-16 23:13:34,025] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:13:34,028] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:13:34,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference
[2023-06-16 23:13:35,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:13:35,399] [INFO] Task started: Prodigal
[2023-06-16 23:13:35,399] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5107291-d51b-4c51-a50e-f9d58c17967f/GCA_009700405.1_ASM970040v1_genomic.fna.gz | prodigal -d GCA_009700405.1_ASM970040v1_genomic.fna/cds.fna -a GCA_009700405.1_ASM970040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:13:39,010] [INFO] Task succeeded: Prodigal
[2023-06-16 23:13:39,010] [INFO] Task started: HMMsearch
[2023-06-16 23:13:39,010] [INFO] Running command: hmmsearch --tblout GCA_009700405.1_ASM970040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference/reference_markers.hmm GCA_009700405.1_ASM970040v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:13:39,212] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:13:39,213] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd5107291-d51b-4c51-a50e-f9d58c17967f/GCA_009700405.1_ASM970040v1_genomic.fna.gz]
[2023-06-16 23:13:39,235] [INFO] Query marker FASTA was written to GCA_009700405.1_ASM970040v1_genomic.fna/markers.fasta
[2023-06-16 23:13:39,236] [INFO] Task started: Blastn
[2023-06-16 23:13:39,236] [INFO] Running command: blastn -query GCA_009700405.1_ASM970040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference/reference_markers.fasta -out GCA_009700405.1_ASM970040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:13:40,295] [INFO] Task succeeded: Blastn
[2023-06-16 23:13:40,300] [INFO] Selected 16 target genomes.
[2023-06-16 23:13:40,301] [INFO] Target genome list was writen to GCA_009700405.1_ASM970040v1_genomic.fna/target_genomes.txt
[2023-06-16 23:13:40,309] [INFO] Task started: fastANI
[2023-06-16 23:13:40,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5107291-d51b-4c51-a50e-f9d58c17967f/GCA_009700405.1_ASM970040v1_genomic.fna.gz --refList GCA_009700405.1_ASM970040v1_genomic.fna/target_genomes.txt --output GCA_009700405.1_ASM970040v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:13:47,790] [INFO] Task succeeded: fastANI
[2023-06-16 23:13:47,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:13:47,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:13:47,794] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:13:47,794] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 23:13:47,794] [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
--------------------------------------------------------------------------------
[2023-06-16 23:13:47,797] [INFO] DFAST Taxonomy check result was written to GCA_009700405.1_ASM970040v1_genomic.fna/tc_result.tsv
[2023-06-16 23:13:47,798] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:13:47,798] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:13:47,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference/checkm_data
[2023-06-16 23:13:47,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:13:47,824] [INFO] Task started: CheckM
[2023-06-16 23:13:47,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009700405.1_ASM970040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009700405.1_ASM970040v1_genomic.fna/checkm_input GCA_009700405.1_ASM970040v1_genomic.fna/checkm_result
[2023-06-16 23:14:06,272] [INFO] Task succeeded: CheckM
[2023-06-16 23:14:06,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:14:06,294] [INFO] ===== Completeness check finished =====
[2023-06-16 23:14:06,295] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:14:06,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009700405.1_ASM970040v1_genomic.fna/markers.fasta)
[2023-06-16 23:14:06,296] [INFO] Task started: Blastn
[2023-06-16 23:14:06,296] [INFO] Running command: blastn -query GCA_009700405.1_ASM970040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2caa9ac8-e059-4481-8be1-a57a0eb26f7d/dqc_reference/reference_markers_gtdb.fasta -out GCA_009700405.1_ASM970040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:14:07,056] [INFO] Task succeeded: Blastn
[2023-06-16 23:14:07,063] [INFO] Selected 14 target genomes.
[2023-06-16 23:14:07,064] [INFO] Target genome list was writen to GCA_009700405.1_ASM970040v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:14:07,072] [INFO] Task started: fastANI
[2023-06-16 23:14:07,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5107291-d51b-4c51-a50e-f9d58c17967f/GCA_009700405.1_ASM970040v1_genomic.fna.gz --refList GCA_009700405.1_ASM970040v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009700405.1_ASM970040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:14:11,501] [INFO] Task succeeded: fastANI
[2023-06-16 23:14:11,510] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:14:11,511] [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_009700405.1	s__QYPT01 sp009700405	99.9998	452	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.18	98.98	0.85	0.81	9	conclusive
GCA_007280125.1	s__QYPT01 sp007280125	94.2791	358	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928745.1	s__QYPT01 sp903928745	80.5972	182	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924485.1	s__QYPT01 sp903924485	80.11	191	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	98.91	98.88	0.87	0.85	3	-
GCA_903834145.1	s__QYPT01 sp903834145	80.0959	197	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.71	99.47	0.95	0.92	23	-
GCA_903822425.1	s__QYPT01 sp903822425	78.2791	101	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	99.86	99.86	0.91	0.91	2	-
GCA_903834705.1	s__QYPT01 sp903834705	78.1266	69	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__QYPT01	95.0	98.91	98.79	0.86	0.80	14	-
GCF_002288185.1	s__Planktophila vernalis	77.4029	56	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014190015.1	s__Planktophila sp014190015	77.2875	66	458	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Planktophila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:14:11,513] [INFO] GTDB search result was written to GCA_009700405.1_ASM970040v1_genomic.fna/result_gtdb.tsv
[2023-06-16 23:14:11,514] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:14:11,517] [INFO] DFAST_QC result json was written to GCA_009700405.1_ASM970040v1_genomic.fna/dqc_result.json
[2023-06-16 23:14:11,517] [INFO] DFAST_QC completed!
[2023-06-16 23:14:11,517] [INFO] Total running time: 0h0m37s