[2024-01-24 12:31:51,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference
[2024-01-24 12:31:52,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,358] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,358] [INFO] Running command: gunzip -c /var/lib/cwl/stgecb7dd19-7b3a-4c68-9bc8-f1782eec2b40/GCF_000429145.1_ASM42914v1_genomic.fna.gz | prodigal -d GCF_000429145.1_ASM42914v1_genomic.fna/cds.fna -a GCF_000429145.1_ASM42914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:02,808] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:02,808] [INFO] Task started: HMMsearch
[2024-01-24 12:32:02,808] [INFO] Running command: hmmsearch --tblout GCF_000429145.1_ASM42914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference/reference_markers.hmm GCF_000429145.1_ASM42914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:03,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:03,122] [INFO] Found 6/6 markers.
[2024-01-24 12:32:03,158] [INFO] Query marker FASTA was written to GCF_000429145.1_ASM42914v1_genomic.fna/markers.fasta
[2024-01-24 12:32:03,159] [INFO] Task started: Blastn
[2024-01-24 12:32:03,159] [INFO] Running command: blastn -query GCF_000429145.1_ASM42914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference/reference_markers.fasta -out GCF_000429145.1_ASM42914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:03,894] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:03,897] [INFO] Selected 26 target genomes.
[2024-01-24 12:32:03,898] [INFO] Target genome list was writen to GCF_000429145.1_ASM42914v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:03,909] [INFO] Task started: fastANI
[2024-01-24 12:32:03,910] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb7dd19-7b3a-4c68-9bc8-f1782eec2b40/GCF_000429145.1_ASM42914v1_genomic.fna.gz --refList GCF_000429145.1_ASM42914v1_genomic.fna/target_genomes.txt --output GCF_000429145.1_ASM42914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:20,987] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:20,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:20,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:21,004] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:21,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:21,004] [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
Aestuariibacter salexigens	strain=DSM 15300	GCA_000429145.1	226010	226010	type	True	100.0	1246	1249	95	conclusive
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	80.2026	81	1249	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	78.8627	100	1249	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.5254	70	1249	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.1638	74	1249	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.1334	74	1249	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	77.9515	82	1249	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.818	99	1249	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	77.5894	70	1249	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	77.5569	85	1249	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	77.4877	122	1249	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	77.0862	65	1249	95	below_threshold
Planctobacterium marinum	strain=K7	GCA_020687805.1	1631968	1631968	type	True	77.0215	66	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:21,006] [INFO] DFAST Taxonomy check result was written to GCF_000429145.1_ASM42914v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:21,007] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:21,007] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:21,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference/checkm_data
[2024-01-24 12:32:21,008] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:21,045] [INFO] Task started: CheckM
[2024-01-24 12:32:21,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429145.1_ASM42914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429145.1_ASM42914v1_genomic.fna/checkm_input GCF_000429145.1_ASM42914v1_genomic.fna/checkm_result
[2024-01-24 12:32:55,987] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:55,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:56,013] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:56,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:56,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429145.1_ASM42914v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:56,015] [INFO] Task started: Blastn
[2024-01-24 12:32:56,015] [INFO] Running command: blastn -query GCF_000429145.1_ASM42914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f1aab6b-2024-48ee-a4dc-4b85e974317b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429145.1_ASM42914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:57,121] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:57,126] [INFO] Selected 22 target genomes.
[2024-01-24 12:32:57,126] [INFO] Target genome list was writen to GCF_000429145.1_ASM42914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:57,141] [INFO] Task started: fastANI
[2024-01-24 12:32:57,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgecb7dd19-7b3a-4c68-9bc8-f1782eec2b40/GCF_000429145.1_ASM42914v1_genomic.fna.gz --refList GCF_000429145.1_ASM42914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429145.1_ASM42914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:11,992] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:12,009] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:12,009] [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_000429145.1	s__Aestuariibacter salexigens	100.0	1246	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aestuariibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000020585.3	s__Alteromonas mediterranea	80.2724	80	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_002807665.1	s__Alteromonas_E facilis	78.8627	100	1249	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_903772925.1	s__Alteromonas macleodii_A	78.6213	73	1249	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	78.5254	70	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_002993325.1	s__Alteromonas gracilis	78.2123	73	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_018531185.1	s__Bowmanella sp018531185	77.9734	67	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Bowmanella	95.0	96.11	96.11	0.88	0.88	2	-
GCF_003584565.2	s__Alteromonas sp002729795	77.9713	97	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCA_017794925.1	s__Alteromonas sp017794925	77.8732	89	1249	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	77.8506	98	1249	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	77.6369	88	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_010500865.1	s__Alteromonas profundi	77.5894	70	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494365.1	s__Alteromonas mangrovi	77.565	93	1249	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	77.5578	85	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002201535.1	s__Lacimicrobium sp002201535	77.2439	70	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014270035.1	s__Neptunicella marina	77.1493	66	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Neptunicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591895.1	s__Lacimicrobium alkaliphilum	76.6568	72	1249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Lacimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:12,011] [INFO] GTDB search result was written to GCF_000429145.1_ASM42914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:12,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:12,016] [INFO] DFAST_QC result json was written to GCF_000429145.1_ASM42914v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:12,016] [INFO] DFAST_QC completed!
[2024-01-24 12:33:12,016] [INFO] Total running time: 0h1m21s