[2024-01-24 11:43:52,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference
[2024-01-24 11:43:53,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:53,988] [INFO] Task started: Prodigal
[2024-01-24 11:43:53,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg28c1e8d1-e045-4e23-bdfe-28b85b994c99/GCF_019249295.1_ASM1924929v1_genomic.fna.gz | prodigal -d GCF_019249295.1_ASM1924929v1_genomic.fna/cds.fna -a GCF_019249295.1_ASM1924929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:06,192] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:06,192] [INFO] Task started: HMMsearch
[2024-01-24 11:44:06,192] [INFO] Running command: hmmsearch --tblout GCF_019249295.1_ASM1924929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference/reference_markers.hmm GCF_019249295.1_ASM1924929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:06,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:06,430] [INFO] Found 6/6 markers.
[2024-01-24 11:44:06,468] [INFO] Query marker FASTA was written to GCF_019249295.1_ASM1924929v1_genomic.fna/markers.fasta
[2024-01-24 11:44:06,468] [INFO] Task started: Blastn
[2024-01-24 11:44:06,468] [INFO] Running command: blastn -query GCF_019249295.1_ASM1924929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference/reference_markers.fasta -out GCF_019249295.1_ASM1924929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:07,182] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:07,185] [INFO] Selected 22 target genomes.
[2024-01-24 11:44:07,185] [INFO] Target genome list was writen to GCF_019249295.1_ASM1924929v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:07,192] [INFO] Task started: fastANI
[2024-01-24 11:44:07,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg28c1e8d1-e045-4e23-bdfe-28b85b994c99/GCF_019249295.1_ASM1924929v1_genomic.fna.gz --refList GCF_019249295.1_ASM1924929v1_genomic.fna/target_genomes.txt --output GCF_019249295.1_ASM1924929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:23,068] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:23,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:23,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:23,080] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:23,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:23,081] [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	100.0	1605	1608	95	conclusive
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	80.3538	265	1608	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	79.1609	252	1608	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.9819	198	1608	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.7455	184	1608	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.6265	190	1608	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.5975	240	1608	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.4348	201	1608	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.3301	215	1608	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.2743	214	1608	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.2386	218	1608	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	77.4139	85	1608	95	below_threshold
Aestuariibacter salexigens	strain=DSM 15300	GCA_000429145.1	226010	226010	type	True	77.3981	102	1608	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	77.2195	127	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:23,082] [INFO] DFAST Taxonomy check result was written to GCF_019249295.1_ASM1924929v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:23,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:23,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:23,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference/checkm_data
[2024-01-24 11:44:23,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:23,132] [INFO] Task started: CheckM
[2024-01-24 11:44:23,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019249295.1_ASM1924929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019249295.1_ASM1924929v1_genomic.fna/checkm_input GCF_019249295.1_ASM1924929v1_genomic.fna/checkm_result
[2024-01-24 11:45:01,798] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:01,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:01,815] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:01,815] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:01,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019249295.1_ASM1924929v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:01,815] [INFO] Task started: Blastn
[2024-01-24 11:45:01,815] [INFO] Running command: blastn -query GCF_019249295.1_ASM1924929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae66c4f-132c-4ee0-a67c-a1da993da474/dqc_reference/reference_markers_gtdb.fasta -out GCF_019249295.1_ASM1924929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:02,939] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:02,942] [INFO] Selected 21 target genomes.
[2024-01-24 11:45:02,942] [INFO] Target genome list was writen to GCF_019249295.1_ASM1924929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:02,955] [INFO] Task started: fastANI
[2024-01-24 11:45:02,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg28c1e8d1-e045-4e23-bdfe-28b85b994c99/GCF_019249295.1_ASM1924929v1_genomic.fna.gz --refList GCF_019249295.1_ASM1924929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019249295.1_ASM1924929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:17,720] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:17,736] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:17,736] [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	100.0	1605	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002993365.1	s__Alteromonas alba	80.4459	262	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	80.1586	215	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_003731635.1	s__Alteromonas oceani	79.1628	251	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	78.9819	198	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCA_019249245.1	s__Alteromonas lipotrueiana	78.9181	164	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500865.1	s__Alteromonas profundi	78.7668	183	1608	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	78.734	249	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	78.6265	190	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_005222225.1	s__Alteromonas lutimaris	78.5917	241	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	78.5872	204	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756315.1	s__Alteromonas sp009811495	78.5112	181	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_001757105.1	s__Alteromonas confluentis	78.3486	214	1608	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	78.2998	204	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000730385.1	s__Alteromonas australica	78.2614	214	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_003584565.2	s__Alteromonas sp002729795	78.2266	250	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCA_002691625.1	s__Alteromonas sp002691625	77.884	183	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_006494365.1	s__Alteromonas mangrovi	77.7946	180	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373625.1	s__Alteromonas sp013373625	77.6979	163	1608	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	77.642	239	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_000429145.1	s__Aestuariibacter salexigens	77.3981	102	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aestuariibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,738] [INFO] GTDB search result was written to GCF_019249295.1_ASM1924929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:17,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:17,743] [INFO] DFAST_QC result json was written to GCF_019249295.1_ASM1924929v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:17,743] [INFO] DFAST_QC completed!
[2024-01-24 11:45:17,743] [INFO] Total running time: 0h1m25s