[2024-01-25 18:57:50,641] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:50,643] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:50,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference
[2024-01-25 18:57:51,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:51,855] [INFO] Task started: Prodigal
[2024-01-25 18:57:51,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b3e48e7-45dd-4f6c-80ac-a0a330f356e7/GCF_025628895.1_ASM2562889v1_genomic.fna.gz | prodigal -d GCF_025628895.1_ASM2562889v1_genomic.fna/cds.fna -a GCF_025628895.1_ASM2562889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:00,294] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:00,295] [INFO] Task started: HMMsearch
[2024-01-25 18:58:00,295] [INFO] Running command: hmmsearch --tblout GCF_025628895.1_ASM2562889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference/reference_markers.hmm GCF_025628895.1_ASM2562889v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:00,519] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:00,520] [INFO] Found 6/6 markers.
[2024-01-25 18:58:00,549] [INFO] Query marker FASTA was written to GCF_025628895.1_ASM2562889v1_genomic.fna/markers.fasta
[2024-01-25 18:58:00,549] [INFO] Task started: Blastn
[2024-01-25 18:58:00,549] [INFO] Running command: blastn -query GCF_025628895.1_ASM2562889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference/reference_markers.fasta -out GCF_025628895.1_ASM2562889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:01,255] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:01,258] [INFO] Selected 23 target genomes.
[2024-01-25 18:58:01,258] [INFO] Target genome list was writen to GCF_025628895.1_ASM2562889v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:01,275] [INFO] Task started: fastANI
[2024-01-25 18:58:01,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b3e48e7-45dd-4f6c-80ac-a0a330f356e7/GCF_025628895.1_ASM2562889v1_genomic.fna.gz --refList GCF_025628895.1_ASM2562889v1_genomic.fna/target_genomes.txt --output GCF_025628895.1_ASM2562889v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:17,408] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:17,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:17,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:17,420] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:58:17,420] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:58:17,421] [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
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	79.0852	410	1175	95	below_threshold
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	78.6838	151	1175	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.6442	183	1175	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	78.6248	171	1175	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.4536	171	1175	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.3935	186	1175	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.3924	216	1175	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.1873	240	1175	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.1618	204	1175	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.1615	268	1175	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.0968	171	1175	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	78.0094	193	1175	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.8608	190	1175	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	76.5347	51	1175	95	below_threshold
Pararheinheimera mesophila	strain=IITR13	GCA_003862465.1	1547515	1547515	type	True	75.6449	54	1175	95	below_threshold
Pararheinheimera mesophila	strain=IITR-13	GCA_000986865.1	1547515	1547515	type	True	75.5798	50	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:17,422] [INFO] DFAST Taxonomy check result was written to GCF_025628895.1_ASM2562889v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:17,422] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:17,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:17,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference/checkm_data
[2024-01-25 18:58:17,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:17,460] [INFO] Task started: CheckM
[2024-01-25 18:58:17,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025628895.1_ASM2562889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025628895.1_ASM2562889v1_genomic.fna/checkm_input GCF_025628895.1_ASM2562889v1_genomic.fna/checkm_result
[2024-01-25 18:58:45,639] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:45,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:45,656] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:45,656] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:45,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025628895.1_ASM2562889v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:45,657] [INFO] Task started: Blastn
[2024-01-25 18:58:45,657] [INFO] Running command: blastn -query GCF_025628895.1_ASM2562889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099fe5e2-3668-4d2d-acdc-167d18109d88/dqc_reference/reference_markers_gtdb.fasta -out GCF_025628895.1_ASM2562889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:46,755] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:46,757] [INFO] Selected 21 target genomes.
[2024-01-25 18:58:46,757] [INFO] Target genome list was writen to GCF_025628895.1_ASM2562889v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:46,771] [INFO] Task started: fastANI
[2024-01-25 18:58:46,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b3e48e7-45dd-4f6c-80ac-a0a330f356e7/GCF_025628895.1_ASM2562889v1_genomic.fna.gz --refList GCF_025628895.1_ASM2562889v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025628895.1_ASM2562889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:02,610] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:02,620] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:59:02,621] [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_019249295.1	s__Alteromonas antoniana	79.0852	410	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911815.1	s__Alteromonas ponticola	78.7119	150	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730385.1	s__Alteromonas australica	78.6442	183	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_000172635.2	s__Alteromonas macleodii	78.3935	186	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_003367475.1	s__Alteromonas aestuariivivens	78.3924	216	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651815.1	s__Alteromonas halophila	78.1756	267	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	78.1641	239	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757105.1	s__Alteromonas confluentis	78.1618	204	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	78.1053	221	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_015644725.1	s__Alteromonas sp015644725	78.0307	232	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	78.0094	193	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	77.8787	189	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249245.1	s__Alteromonas lipotrueiana	77.873	155	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222405.1	s__Alteromonas sp018222405	77.5598	171	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	77.5259	178	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_002591895.1	s__Lacimicrobium alkaliphilum	76.8102	77	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:02,622] [INFO] GTDB search result was written to GCF_025628895.1_ASM2562889v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:02,622] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:02,625] [INFO] DFAST_QC result json was written to GCF_025628895.1_ASM2562889v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:02,626] [INFO] DFAST_QC completed!
[2024-01-25 18:59:02,626] [INFO] Total running time: 0h1m12s