[2024-01-24 14:05:53,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference
[2024-01-24 14:05:55,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,363] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f27a3cf-86da-40ad-a5e1-d309c8967a8d/GCF_014651815.1_ASM1465181v1_genomic.fna.gz | prodigal -d GCF_014651815.1_ASM1465181v1_genomic.fna/cds.fna -a GCF_014651815.1_ASM1465181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:06,961] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:06,962] [INFO] Task started: HMMsearch
[2024-01-24 14:06:06,962] [INFO] Running command: hmmsearch --tblout GCF_014651815.1_ASM1465181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference/reference_markers.hmm GCF_014651815.1_ASM1465181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:07,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:07,364] [INFO] Found 6/6 markers.
[2024-01-24 14:06:07,412] [INFO] Query marker FASTA was written to GCF_014651815.1_ASM1465181v1_genomic.fna/markers.fasta
[2024-01-24 14:06:07,413] [INFO] Task started: Blastn
[2024-01-24 14:06:07,413] [INFO] Running command: blastn -query GCF_014651815.1_ASM1465181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference/reference_markers.fasta -out GCF_014651815.1_ASM1465181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:08,231] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:08,234] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:08,235] [INFO] Target genome list was writen to GCF_014651815.1_ASM1465181v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:08,250] [INFO] Task started: fastANI
[2024-01-24 14:06:08,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f27a3cf-86da-40ad-a5e1-d309c8967a8d/GCF_014651815.1_ASM1465181v1_genomic.fna.gz --refList GCF_014651815.1_ASM1465181v1_genomic.fna/target_genomes.txt --output GCF_014651815.1_ASM1465181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:25,689] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:25,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:25,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:25,700] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:25,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:25,701] [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 halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	100.0	1297	1299	95	conclusive
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.8383	197	1299	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	78.7234	193	1299	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.5931	296	1299	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	78.5512	137	1299	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.3121	192	1299	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.1757	247	1299	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.1163	174	1299	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	78.0404	178	1299	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.9673	159	1299	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	77.9365	170	1299	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	77.2236	88	1299	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	75.7324	51	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:25,703] [INFO] DFAST Taxonomy check result was written to GCF_014651815.1_ASM1465181v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:25,703] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:25,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:25,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference/checkm_data
[2024-01-24 14:06:25,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:25,749] [INFO] Task started: CheckM
[2024-01-24 14:06:25,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651815.1_ASM1465181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651815.1_ASM1465181v1_genomic.fna/checkm_input GCF_014651815.1_ASM1465181v1_genomic.fna/checkm_result
[2024-01-24 14:07:03,192] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:03,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,218] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:03,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:03,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651815.1_ASM1465181v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:03,219] [INFO] Task started: Blastn
[2024-01-24 14:07:03,219] [INFO] Running command: blastn -query GCF_014651815.1_ASM1465181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d884d97-fc16-4c09-91e0-46f51df80966/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651815.1_ASM1465181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:04,370] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:04,374] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:04,374] [INFO] Target genome list was writen to GCF_014651815.1_ASM1465181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:04,399] [INFO] Task started: fastANI
[2024-01-24 14:07:04,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f27a3cf-86da-40ad-a5e1-d309c8967a8d/GCF_014651815.1_ASM1465181v1_genomic.fna.gz --refList GCF_014651815.1_ASM1465181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651815.1_ASM1465181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:19,419] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,434] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:19,434] [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_014651815.1	s__Alteromonas halophila	100.0	1297	1299	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_006228385.1	s__Alteromonas iocasae	78.8383	197	1299	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	78.7234	193	1299	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	78.6676	155	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249295.1	s__Alteromonas antoniana	78.5824	298	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	78.523	141	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_016405965.1	s__Alteromonas sp016405965	78.4132	166	1299	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	78.3161	207	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_003367475.1	s__Alteromonas aestuariivivens	78.3121	192	1299	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	78.171	248	1299	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	78.0519	179	1299	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	77.9367	170	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644725.1	s__Alteromonas sp015644725	77.8663	206	1299	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	77.8361	180	1299	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	77.5227	167	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_006494365.1	s__Alteromonas mangrovi	77.4704	146	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691625.1	s__Alteromonas sp002691625	77.3376	146	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	76.4713	118	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018199995.1	s__Photobacterium sp018199995	76.0751	59	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,436] [INFO] GTDB search result was written to GCF_014651815.1_ASM1465181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:19,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:19,440] [INFO] DFAST_QC result json was written to GCF_014651815.1_ASM1465181v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:19,440] [INFO] DFAST_QC completed!
[2024-01-24 14:07:19,440] [INFO] Total running time: 0h1m25s