[2024-01-24 12:06:13,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference
[2024-01-24 12:06:14,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,771] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ab246dd-4ceb-45f8-97ec-3e576d6407be/GCF_018474025.1_ASM1847402v1_genomic.fna.gz | prodigal -d GCF_018474025.1_ASM1847402v1_genomic.fna/cds.fna -a GCF_018474025.1_ASM1847402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,207] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,208] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,208] [INFO] Running command: hmmsearch --tblout GCF_018474025.1_ASM1847402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference/reference_markers.hmm GCF_018474025.1_ASM1847402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,583] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ab246dd-4ceb-45f8-97ec-3e576d6407be/GCF_018474025.1_ASM1847402v1_genomic.fna.gz]
[2024-01-24 12:06:25,615] [INFO] Query marker FASTA was written to GCF_018474025.1_ASM1847402v1_genomic.fna/markers.fasta
[2024-01-24 12:06:25,615] [INFO] Task started: Blastn
[2024-01-24 12:06:25,615] [INFO] Running command: blastn -query GCF_018474025.1_ASM1847402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference/reference_markers.fasta -out GCF_018474025.1_ASM1847402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,297] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,301] [INFO] Selected 23 target genomes.
[2024-01-24 12:06:26,301] [INFO] Target genome list was writen to GCF_018474025.1_ASM1847402v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,310] [INFO] Task started: fastANI
[2024-01-24 12:06:26,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ab246dd-4ceb-45f8-97ec-3e576d6407be/GCF_018474025.1_ASM1847402v1_genomic.fna.gz --refList GCF_018474025.1_ASM1847402v1_genomic.fna/target_genomes.txt --output GCF_018474025.1_ASM1847402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:42,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:42,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:42,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:42,448] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:42,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:42,448] [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 oceanisediminis	strain=SM 2104	GCA_018474025.1	2836180	2836180	type	True	100.0	1264	1264	95	conclusive
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.0776	79	1264	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.9343	78	1264	95	below_threshold
Alteromonas flava	strain=P0211	GCA_002807685.1	2048003	2048003	type	True	78.462	145	1264	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.9932	100	1264	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.9704	95	1264	95	below_threshold
Alteromonas sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	77.9153	66	1264	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.8259	72	1264	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	77.788	80	1264	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	77.7805	155	1264	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	77.6862	70	1264	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	77.654	72	1264	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.4656	75	1264	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.4392	83	1264	95	below_threshold
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	77.3303	73	1264	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.0953	84	1264	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	76.8386	56	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:42,450] [INFO] DFAST Taxonomy check result was written to GCF_018474025.1_ASM1847402v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:42,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:42,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:42,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference/checkm_data
[2024-01-24 12:06:42,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:42,492] [INFO] Task started: CheckM
[2024-01-24 12:06:42,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018474025.1_ASM1847402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018474025.1_ASM1847402v1_genomic.fna/checkm_input GCF_018474025.1_ASM1847402v1_genomic.fna/checkm_result
[2024-01-24 12:07:18,966] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:18,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:18,990] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:18,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:18,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018474025.1_ASM1847402v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:18,991] [INFO] Task started: Blastn
[2024-01-24 12:07:18,991] [INFO] Running command: blastn -query GCF_018474025.1_ASM1847402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99e2972-d4f1-4fce-a69c-74f080c9c940/dqc_reference/reference_markers_gtdb.fasta -out GCF_018474025.1_ASM1847402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:19,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:19,934] [INFO] Selected 24 target genomes.
[2024-01-24 12:07:19,934] [INFO] Target genome list was writen to GCF_018474025.1_ASM1847402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:19,953] [INFO] Task started: fastANI
[2024-01-24 12:07:19,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ab246dd-4ceb-45f8-97ec-3e576d6407be/GCF_018474025.1_ASM1847402v1_genomic.fna.gz --refList GCF_018474025.1_ASM1847402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018474025.1_ASM1847402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:35,503] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,523] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:35,523] [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_018474025.1	s__Alteromonas_E sp018474025	100.0	1264	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000730385.1	s__Alteromonas australica	80.0776	79	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_003429285.1	s__Alteromonas sediminis	79.1457	79	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_003203515.1	s__Glaciecola sp003203515	78.5263	57	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807685.1	s__Alteromonas_E flava	78.4631	146	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538345.1	s__Alteromonas sp006538345	78.1056	56	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019249295.1	s__Alteromonas antoniana	77.9932	100	1264	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	77.9759	97	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003820355.1	s__Alteromonas_F sediminis	77.9257	67	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	77.908	75	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_000597705.1	s__Alteromonas sp000597705	77.881	66	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_003367475.1	s__Alteromonas aestuariivivens	77.788	80	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807665.1	s__Alteromonas_E facilis	77.7751	154	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	77.6912	71	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001660395.1	s__XY-R5 sp001660395	77.6329	66	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__XY-R5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373625.1	s__Alteromonas sp013373625	77.5285	80	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	77.4741	74	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005222225.1	s__Alteromonas lutimaris	77.4392	83	1264	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	77.3303	73	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	77.228	69	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_014651815.1	s__Alteromonas halophila	77.1153	85	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,525] [INFO] GTDB search result was written to GCF_018474025.1_ASM1847402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:35,526] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:35,533] [INFO] DFAST_QC result json was written to GCF_018474025.1_ASM1847402v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:35,534] [INFO] DFAST_QC completed!
[2024-01-24 12:07:35,534] [INFO] Total running time: 0h1m22s