[2024-01-24 15:26:33,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,111] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,111] [INFO] DQC Reference Directory: /var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference
[2024-01-24 15:26:35,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:35,764] [INFO] Task started: Prodigal
[2024-01-24 15:26:35,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d874867-a931-450a-ad3f-f64d6551088e/GCF_003367475.1_ASM336747v1_genomic.fna.gz | prodigal -d GCF_003367475.1_ASM336747v1_genomic.fna/cds.fna -a GCF_003367475.1_ASM336747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:46,524] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:46,525] [INFO] Task started: HMMsearch
[2024-01-24 15:26:46,525] [INFO] Running command: hmmsearch --tblout GCF_003367475.1_ASM336747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference/reference_markers.hmm GCF_003367475.1_ASM336747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:46,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:46,831] [INFO] Found 6/6 markers.
[2024-01-24 15:26:46,863] [INFO] Query marker FASTA was written to GCF_003367475.1_ASM336747v1_genomic.fna/markers.fasta
[2024-01-24 15:26:46,863] [INFO] Task started: Blastn
[2024-01-24 15:26:46,864] [INFO] Running command: blastn -query GCF_003367475.1_ASM336747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference/reference_markers.fasta -out GCF_003367475.1_ASM336747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:47,648] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:47,652] [INFO] Selected 23 target genomes.
[2024-01-24 15:26:47,653] [INFO] Target genome list was writen to GCF_003367475.1_ASM336747v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:47,758] [INFO] Task started: fastANI
[2024-01-24 15:26:47,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d874867-a931-450a-ad3f-f64d6551088e/GCF_003367475.1_ASM336747v1_genomic.fna.gz --refList GCF_003367475.1_ASM336747v1_genomic.fna/target_genomes.txt --output GCF_003367475.1_ASM336747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:03,489] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:03,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:03,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:03,505] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:03,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:03,505] [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 aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	100.0	1264	1266	95	conclusive
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.0204	133	1266	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.6155	142	1266	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.6148	134	1266	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.5459	142	1266	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.4043	197	1266	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.2518	177	1266	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.1855	142	1266	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.1276	235	1266	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.9676	207	1266	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	77.9611	221	1266	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	77.9329	172	1266	95	below_threshold
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	77.9121	138	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:03,507] [INFO] DFAST Taxonomy check result was written to GCF_003367475.1_ASM336747v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:03,507] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:03,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:03,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference/checkm_data
[2024-01-24 15:27:03,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:03,548] [INFO] Task started: CheckM
[2024-01-24 15:27:03,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367475.1_ASM336747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367475.1_ASM336747v1_genomic.fna/checkm_input GCF_003367475.1_ASM336747v1_genomic.fna/checkm_result
[2024-01-24 15:27:40,408] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:40,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:40,427] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:40,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:40,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367475.1_ASM336747v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:40,428] [INFO] Task started: Blastn
[2024-01-24 15:27:40,428] [INFO] Running command: blastn -query GCF_003367475.1_ASM336747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad961c4-3415-41a4-80e4-5d979eb36072/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367475.1_ASM336747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:41,713] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:41,717] [INFO] Selected 22 target genomes.
[2024-01-24 15:27:41,717] [INFO] Target genome list was writen to GCF_003367475.1_ASM336747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:41,734] [INFO] Task started: fastANI
[2024-01-24 15:27:41,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d874867-a931-450a-ad3f-f64d6551088e/GCF_003367475.1_ASM336747v1_genomic.fna.gz --refList GCF_003367475.1_ASM336747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367475.1_ASM336747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:57,587] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:57,601] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:57,602] [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_003367475.1	s__Alteromonas aestuariivivens	100.0	1264	1266	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_002993325.1	s__Alteromonas gracilis	78.9858	134	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_003429285.1	s__Alteromonas sediminis	78.5911	146	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_000730385.1	s__Alteromonas australica	78.5542	142	1266	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	78.5526	136	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_001953635.1	s__Alteromonas abrolhosensis	78.5459	142	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_001757105.1	s__Alteromonas confluentis	78.4043	197	1266	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	78.2824	214	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_900129565.1	s__Alteromonas aggregata	78.2766	156	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCF_000808575.1	s__Alteromonas marina	78.2512	145	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_010500865.1	s__Alteromonas profundi	78.2124	141	1266	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	78.2007	176	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019249295.1	s__Alteromonas antoniana	78.1399	235	1266	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	77.9767	220	1266	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	77.9676	207	1266	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	77.9329	172	1266	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	77.9121	138	1266	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 15:27:57,603] [INFO] GTDB search result was written to GCF_003367475.1_ASM336747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:57,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:57,608] [INFO] DFAST_QC result json was written to GCF_003367475.1_ASM336747v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:57,608] [INFO] DFAST_QC completed!
[2024-01-24 15:27:57,608] [INFO] Total running time: 0h1m25s