[2024-01-24 13:41:40,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,479] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference
[2024-01-24 13:41:41,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,752] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f8073ed-34f5-49a2-b24d-73575220d63d/GCF_003820355.1_ASM382035v1_genomic.fna.gz | prodigal -d GCF_003820355.1_ASM382035v1_genomic.fna/cds.fna -a GCF_003820355.1_ASM382035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:52,501] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:52,502] [INFO] Task started: HMMsearch
[2024-01-24 13:41:52,502] [INFO] Running command: hmmsearch --tblout GCF_003820355.1_ASM382035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference/reference_markers.hmm GCF_003820355.1_ASM382035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:52,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:52,819] [INFO] Found 6/6 markers.
[2024-01-24 13:41:52,858] [INFO] Query marker FASTA was written to GCF_003820355.1_ASM382035v1_genomic.fna/markers.fasta
[2024-01-24 13:41:52,858] [INFO] Task started: Blastn
[2024-01-24 13:41:52,858] [INFO] Running command: blastn -query GCF_003820355.1_ASM382035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference/reference_markers.fasta -out GCF_003820355.1_ASM382035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,574] [INFO] Selected 28 target genomes.
[2024-01-24 13:41:53,574] [INFO] Target genome list was writen to GCF_003820355.1_ASM382035v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:53,591] [INFO] Task started: fastANI
[2024-01-24 13:41:53,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8073ed-34f5-49a2-b24d-73575220d63d/GCF_003820355.1_ASM382035v1_genomic.fna.gz --refList GCF_003820355.1_ASM382035v1_genomic.fna/target_genomes.txt --output GCF_003820355.1_ASM382035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:11,655] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:11,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:11,678] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:11,678] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:11,678] [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 sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	100.0	1316	1316	95	conclusive
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	78.8578	68	1316	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.5939	82	1316	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.282	82	1316	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	78.2443	75	1316	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	78.1725	87	1316	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.0225	95	1316	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.9127	98	1316	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	77.9015	93	1316	95	below_threshold
Planctobacterium marinum	strain=K7	GCA_020687805.1	1631968	1631968	type	True	77.6236	60	1316	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	77.5755	103	1316	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	76.9514	61	1316	95	below_threshold
Bowmanella pacifica	strain=CGMCC 1.7086	GCA_014645355.1	502051	502051	type	True	76.9279	57	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,680] [INFO] DFAST Taxonomy check result was written to GCF_003820355.1_ASM382035v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:11,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:11,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:11,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference/checkm_data
[2024-01-24 13:42:11,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:11,721] [INFO] Task started: CheckM
[2024-01-24 13:42:11,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003820355.1_ASM382035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003820355.1_ASM382035v1_genomic.fna/checkm_input GCF_003820355.1_ASM382035v1_genomic.fna/checkm_result
[2024-01-24 13:42:46,195] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:46,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:46,219] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:46,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:46,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003820355.1_ASM382035v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:46,220] [INFO] Task started: Blastn
[2024-01-24 13:42:46,220] [INFO] Running command: blastn -query GCF_003820355.1_ASM382035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb93a411-b5b6-46c2-8727-fd27d11f995c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003820355.1_ASM382035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:47,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:47,263] [INFO] Selected 27 target genomes.
[2024-01-24 13:42:47,263] [INFO] Target genome list was writen to GCF_003820355.1_ASM382035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:47,346] [INFO] Task started: fastANI
[2024-01-24 13:42:47,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8073ed-34f5-49a2-b24d-73575220d63d/GCF_003820355.1_ASM382035v1_genomic.fna.gz --refList GCF_003820355.1_ASM382035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003820355.1_ASM382035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:08,835] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:08,856] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:08,856] [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_003820355.1	s__Alteromonas_F sediminis	100.0	1316	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003584565.2	s__Alteromonas sp002729795	78.7048	69	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_018860965.1	s__Alteromonas sp018860965	78.5767	79	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860805.1	s__Alteromonas sp018860805	78.327	70	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500895.1	s__Alteromonas genovensis	78.236	83	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	-
GCF_000730385.1	s__Alteromonas australica	78.2324	85	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCA_013373625.1	s__Alteromonas sp013373625	78.2183	88	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538345.1	s__Alteromonas sp006538345	78.1733	85	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129565.1	s__Alteromonas aggregata	77.9756	95	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCF_001757105.1	s__Alteromonas confluentis	77.9015	93	1316	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	77.8753	61	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__XY-R5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	77.8678	86	1316	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	77.8254	78	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_009811415.1	s__Alteromonas sp009811415	77.77	84	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	77.5832	102	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCA_017794925.1	s__Alteromonas sp017794925	77.5507	89	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	76.9514	61	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_001466725.1	s__Lacimicrobium alkaliphilum_B	76.7661	54	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:08,858] [INFO] GTDB search result was written to GCF_003820355.1_ASM382035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:08,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:08,864] [INFO] DFAST_QC result json was written to GCF_003820355.1_ASM382035v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:08,864] [INFO] DFAST_QC completed!
[2024-01-24 13:43:08,864] [INFO] Total running time: 0h1m28s