[2024-01-24 13:36:31,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference
[2024-01-24 13:36:33,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,309] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,309] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb98cf5d-1157-4011-a8d1-e598a904c2cb/GCF_020736705.1_ASM2073670v1_genomic.fna.gz | prodigal -d GCF_020736705.1_ASM2073670v1_genomic.fna/cds.fna -a GCF_020736705.1_ASM2073670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:41,089] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:41,090] [INFO] Task started: HMMsearch
[2024-01-24 13:36:41,090] [INFO] Running command: hmmsearch --tblout GCF_020736705.1_ASM2073670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference/reference_markers.hmm GCF_020736705.1_ASM2073670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:41,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:41,357] [INFO] Found 6/6 markers.
[2024-01-24 13:36:41,388] [INFO] Query marker FASTA was written to GCF_020736705.1_ASM2073670v1_genomic.fna/markers.fasta
[2024-01-24 13:36:41,389] [INFO] Task started: Blastn
[2024-01-24 13:36:41,389] [INFO] Running command: blastn -query GCF_020736705.1_ASM2073670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference/reference_markers.fasta -out GCF_020736705.1_ASM2073670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:42,041] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:42,045] [INFO] Selected 11 target genomes.
[2024-01-24 13:36:42,046] [INFO] Target genome list was writen to GCF_020736705.1_ASM2073670v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:42,060] [INFO] Task started: fastANI
[2024-01-24 13:36:42,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb98cf5d-1157-4011-a8d1-e598a904c2cb/GCF_020736705.1_ASM2073670v1_genomic.fna.gz --refList GCF_020736705.1_ASM2073670v1_genomic.fna/target_genomes.txt --output GCF_020736705.1_ASM2073670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:50,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:50,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:50,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:50,268] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:50,268] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:50,268] [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
Psychrobacter sanguinis	strain=FDAARGOS_1598	GCA_020736705.1	861445	861445	type	True	100.0	1127	1130	95	conclusive
Psychrobacter phenylpyruvicus	strain=NCTC10526	GCA_900455955.1	29432	29432	type	True	83.1139	674	1130	95	below_threshold
Psychrobacter phenylpyruvicus	strain=DSM 7000	GCA_000685805.1	29432	29432	type	True	82.7879	654	1130	95	below_threshold
Psychrobacter phenylpyruvicus	strain=NBRC 102152	GCA_001591185.1	29432	29432	type	True	82.6189	645	1130	95	below_threshold
Psychrobacter lutiphocae	strain=DSM 21542	GCA_000382145.1	540500	540500	type	True	78.8895	317	1130	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	77.83	133	1130	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	77.8265	187	1130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:50,269] [INFO] DFAST Taxonomy check result was written to GCF_020736705.1_ASM2073670v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:50,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:50,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:50,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference/checkm_data
[2024-01-24 13:36:50,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:50,304] [INFO] Task started: CheckM
[2024-01-24 13:36:50,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020736705.1_ASM2073670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020736705.1_ASM2073670v1_genomic.fna/checkm_input GCF_020736705.1_ASM2073670v1_genomic.fna/checkm_result
[2024-01-24 13:37:20,108] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:20,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:20,128] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:20,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:20,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020736705.1_ASM2073670v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:20,129] [INFO] Task started: Blastn
[2024-01-24 13:37:20,129] [INFO] Running command: blastn -query GCF_020736705.1_ASM2073670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fc48017-ae4c-4c04-8bc3-b82b9b31fb57/dqc_reference/reference_markers_gtdb.fasta -out GCF_020736705.1_ASM2073670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:20,994] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:20,997] [INFO] Selected 8 target genomes.
[2024-01-24 13:37:20,997] [INFO] Target genome list was writen to GCF_020736705.1_ASM2073670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:21,011] [INFO] Task started: fastANI
[2024-01-24 13:37:21,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb98cf5d-1157-4011-a8d1-e598a904c2cb/GCF_020736705.1_ASM2073670v1_genomic.fna.gz --refList GCF_020736705.1_ASM2073670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020736705.1_ASM2073670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:27,360] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:27,369] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:27,369] [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
GCF_904846495.1	s__Psychrobacter sanguinis	96.9577	925	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.88	96.57	0.90	0.89	7	conclusive
GCF_900162825.1	s__Psychrobacter piechaudii	83.6271	575	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385225.1	s__Psychrobacter sp002385225	83.521	647	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685805.1	s__Psychrobacter phenylpyruvicus	82.7854	654	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	99.99	1.00	0.99	4	-
GCF_900162815.1	s__Psychrobacter pasteurii	82.1253	600	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725675.1	s__Psychrobacter sanguinis_A	80.0616	480	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.56	98.43	0.91	0.90	4	-
GCA_018260395.1	s__Psychrobacter sp018260395	79.8786	388	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002313155.2	s__Psychrobacter sp002313155	79.621	394	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:27,371] [INFO] GTDB search result was written to GCF_020736705.1_ASM2073670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:27,371] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:27,375] [INFO] DFAST_QC result json was written to GCF_020736705.1_ASM2073670v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:27,375] [INFO] DFAST_QC completed!
[2024-01-24 13:37:27,375] [INFO] Total running time: 0h0m55s