[2024-01-24 12:28:34,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,939] [INFO] DQC Reference Directory: /var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference
[2024-01-24 12:28:36,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,146] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg54f65bd7-f9fe-40d6-bb22-c58989d69cba/GCF_900455955.1_52121_C02_genomic.fna.gz | prodigal -d GCF_900455955.1_52121_C02_genomic.fna/cds.fna -a GCF_900455955.1_52121_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:43,240] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:43,241] [INFO] Task started: HMMsearch
[2024-01-24 12:28:43,241] [INFO] Running command: hmmsearch --tblout GCF_900455955.1_52121_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference/reference_markers.hmm GCF_900455955.1_52121_C02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:43,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:43,503] [INFO] Found 6/6 markers.
[2024-01-24 12:28:43,532] [INFO] Query marker FASTA was written to GCF_900455955.1_52121_C02_genomic.fna/markers.fasta
[2024-01-24 12:28:43,532] [INFO] Task started: Blastn
[2024-01-24 12:28:43,532] [INFO] Running command: blastn -query GCF_900455955.1_52121_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference/reference_markers.fasta -out GCF_900455955.1_52121_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:44,162] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:44,167] [INFO] Selected 10 target genomes.
[2024-01-24 12:28:44,167] [INFO] Target genome list was writen to GCF_900455955.1_52121_C02_genomic.fna/target_genomes.txt
[2024-01-24 12:28:44,218] [INFO] Task started: fastANI
[2024-01-24 12:28:44,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg54f65bd7-f9fe-40d6-bb22-c58989d69cba/GCF_900455955.1_52121_C02_genomic.fna.gz --refList GCF_900455955.1_52121_C02_genomic.fna/target_genomes.txt --output GCF_900455955.1_52121_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:51,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:51,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:51,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:51,722] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:28:51,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:28:51,722] [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 phenylpyruvicus	strain=NCTC10526	GCA_900455955.1	29432	29432	type	True	100.0	1132	1145	95	conclusive
Psychrobacter phenylpyruvicus	strain=DSM 7000	GCA_000685805.1	29432	29432	type	True	99.8756	976	1145	95	conclusive
Psychrobacter phenylpyruvicus	strain=NBRC 102152	GCA_001591185.1	29432	29432	type	True	99.851	928	1145	95	conclusive
Psychrobacter sanguinis	strain=FDAARGOS_1598	GCA_020736705.1	861445	861445	type	True	83.2189	682	1145	95	below_threshold
Psychrobacter lutiphocae	strain=DSM 21542	GCA_000382145.1	540500	540500	type	True	79.2564	348	1145	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	77.404	143	1145	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	77.2251	149	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:51,724] [INFO] DFAST Taxonomy check result was written to GCF_900455955.1_52121_C02_genomic.fna/tc_result.tsv
[2024-01-24 12:28:51,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:51,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:51,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference/checkm_data
[2024-01-24 12:28:51,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:51,761] [INFO] Task started: CheckM
[2024-01-24 12:28:51,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900455955.1_52121_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900455955.1_52121_C02_genomic.fna/checkm_input GCF_900455955.1_52121_C02_genomic.fna/checkm_result
[2024-01-24 12:29:19,004] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:19,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:19,029] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:19,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:19,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900455955.1_52121_C02_genomic.fna/markers.fasta)
[2024-01-24 12:29:19,030] [INFO] Task started: Blastn
[2024-01-24 12:29:19,030] [INFO] Running command: blastn -query GCF_900455955.1_52121_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stgda3cf87d-973d-4a15-ae1d-5b2ed070327b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900455955.1_52121_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:19,985] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:19,990] [INFO] Selected 6 target genomes.
[2024-01-24 12:29:19,991] [INFO] Target genome list was writen to GCF_900455955.1_52121_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:20,013] [INFO] Task started: fastANI
[2024-01-24 12:29:20,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg54f65bd7-f9fe-40d6-bb22-c58989d69cba/GCF_900455955.1_52121_C02_genomic.fna.gz --refList GCF_900455955.1_52121_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900455955.1_52121_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:24,798] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:24,809] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:24,809] [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_000685805.1	s__Psychrobacter phenylpyruvicus	99.8756	976	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	99.99	1.00	0.99	4	conclusive
GCA_002385225.1	s__Psychrobacter sp002385225	89.0675	781	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162825.1	s__Psychrobacter piechaudii	88.7928	670	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162815.1	s__Psychrobacter pasteurii	84.8985	659	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846495.1	s__Psychrobacter sanguinis	82.732	671	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.88	96.57	0.90	0.89	7	-
GCF_009725675.1	s__Psychrobacter sanguinis_A	80.2256	496	1145	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.56	98.43	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:24,811] [INFO] GTDB search result was written to GCF_900455955.1_52121_C02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:24,811] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:24,814] [INFO] DFAST_QC result json was written to GCF_900455955.1_52121_C02_genomic.fna/dqc_result.json
[2024-01-24 12:29:24,814] [INFO] DFAST_QC completed!
[2024-01-24 12:29:24,815] [INFO] Total running time: 0h0m50s