[2024-01-24 12:39:48,296] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:48,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:48,298] [INFO] DQC Reference Directory: /var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference
[2024-01-24 12:39:49,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:49,467] [INFO] Task started: Prodigal
[2024-01-24 12:39:49,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg400eb1a8-9474-4351-879e-aef2cd447f71/GCF_030159935.1_ASM3015993v1_genomic.fna.gz | prodigal -d GCF_030159935.1_ASM3015993v1_genomic.fna/cds.fna -a GCF_030159935.1_ASM3015993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:58,336] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:58,336] [INFO] Task started: HMMsearch
[2024-01-24 12:39:58,336] [INFO] Running command: hmmsearch --tblout GCF_030159935.1_ASM3015993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference/reference_markers.hmm GCF_030159935.1_ASM3015993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:58,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:58,544] [INFO] Found 6/6 markers.
[2024-01-24 12:39:58,573] [INFO] Query marker FASTA was written to GCF_030159935.1_ASM3015993v1_genomic.fna/markers.fasta
[2024-01-24 12:39:58,574] [INFO] Task started: Blastn
[2024-01-24 12:39:58,574] [INFO] Running command: blastn -query GCF_030159935.1_ASM3015993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference/reference_markers.fasta -out GCF_030159935.1_ASM3015993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:59,287] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:59,291] [INFO] Selected 32 target genomes.
[2024-01-24 12:39:59,291] [INFO] Target genome list was writen to GCF_030159935.1_ASM3015993v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:59,301] [INFO] Task started: fastANI
[2024-01-24 12:39:59,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg400eb1a8-9474-4351-879e-aef2cd447f71/GCF_030159935.1_ASM3015993v1_genomic.fna.gz --refList GCF_030159935.1_ASM3015993v1_genomic.fna/target_genomes.txt --output GCF_030159935.1_ASM3015993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:17,654] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:17,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:17,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:17,666] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:17,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:17,666] [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
Algimonas arctica	strain=KCTC 32513	GCA_014652695.1	1479486	1479486	type	True	77.1077	216	1045	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	76.2057	57	1045	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.1387	54	1045	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.1386	54	1045	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.0485	63	1045	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	75.9699	63	1045	95	below_threshold
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	75.9428	72	1045	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	75.819	53	1045	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	75.3379	53	1045	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	75.203	58	1045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:17,670] [INFO] DFAST Taxonomy check result was written to GCF_030159935.1_ASM3015993v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:17,671] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:17,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:17,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference/checkm_data
[2024-01-24 12:40:17,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:17,706] [INFO] Task started: CheckM
[2024-01-24 12:40:17,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159935.1_ASM3015993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159935.1_ASM3015993v1_genomic.fna/checkm_input GCF_030159935.1_ASM3015993v1_genomic.fna/checkm_result
[2024-01-24 12:40:47,670] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:47,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:47,688] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:47,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:47,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159935.1_ASM3015993v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:47,688] [INFO] Task started: Blastn
[2024-01-24 12:40:47,689] [INFO] Running command: blastn -query GCF_030159935.1_ASM3015993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5731ba3-e090-4f06-9334-1a57ce07cc24/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159935.1_ASM3015993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:48,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:48,995] [INFO] Selected 32 target genomes.
[2024-01-24 12:40:48,995] [INFO] Target genome list was writen to GCF_030159935.1_ASM3015993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:49,031] [INFO] Task started: fastANI
[2024-01-24 12:40:49,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg400eb1a8-9474-4351-879e-aef2cd447f71/GCF_030159935.1_ASM3015993v1_genomic.fna.gz --refList GCF_030159935.1_ASM3015993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159935.1_ASM3015993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:08,023] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:08,033] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:08,033] [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_014652695.1	s__Litorimonas arctica	77.1077	216	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	76.2409	68	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	76.2057	57	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_002088945.1	s__Henriciella pelagia	76.1387	54	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017792385.1	s__Hyphomonas sp017792385	76.056	54	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103475.1	s__Maricaulis salignorans	75.9699	63	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	75.8531	55	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791775.1	s__Hyphomonas sp013791775	75.7631	58	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.98	99.96	1.00	0.99	4	-
GCF_900112185.1	s__Bosea sp900112185	75.4993	54	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428755.1	s__Bosea sp016428755	75.4753	52	1045	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:08,036] [INFO] GTDB search result was written to GCF_030159935.1_ASM3015993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:08,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:08,040] [INFO] DFAST_QC result json was written to GCF_030159935.1_ASM3015993v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:08,041] [INFO] DFAST_QC completed!
[2024-01-24 12:41:08,041] [INFO] Total running time: 0h1m20s