[2024-01-24 13:55:19,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference
[2024-01-24 13:55:21,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,231] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,232] [INFO] Running command: gunzip -c /var/lib/cwl/stg9904282f-132f-448d-b30a-414cdcc87671/GCF_002499975.2_ASM249997v2_genomic.fna.gz | prodigal -d GCF_002499975.2_ASM249997v2_genomic.fna/cds.fna -a GCF_002499975.2_ASM249997v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,015] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,015] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,015] [INFO] Running command: hmmsearch --tblout GCF_002499975.2_ASM249997v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference/reference_markers.hmm GCF_002499975.2_ASM249997v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:32,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:32,347] [INFO] Found 6/6 markers.
[2024-01-24 13:55:32,384] [INFO] Query marker FASTA was written to GCF_002499975.2_ASM249997v2_genomic.fna/markers.fasta
[2024-01-24 13:55:32,385] [INFO] Task started: Blastn
[2024-01-24 13:55:32,385] [INFO] Running command: blastn -query GCF_002499975.2_ASM249997v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference/reference_markers.fasta -out GCF_002499975.2_ASM249997v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:33,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:33,068] [INFO] Selected 27 target genomes.
[2024-01-24 13:55:33,068] [INFO] Target genome list was writen to GCF_002499975.2_ASM249997v2_genomic.fna/target_genomes.txt
[2024-01-24 13:55:33,078] [INFO] Task started: fastANI
[2024-01-24 13:55:33,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg9904282f-132f-448d-b30a-414cdcc87671/GCF_002499975.2_ASM249997v2_genomic.fna.gz --refList GCF_002499975.2_ASM249997v2_genomic.fna/target_genomes.txt --output GCF_002499975.2_ASM249997v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:52,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:52,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:52,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:52,264] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:52,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:52,265] [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 pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	100.0	1435	1438	95	conclusive
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	79.0233	172	1438	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	78.7569	143	1438	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.4695	146	1438	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.3146	137	1438	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.2599	156	1438	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.2545	199	1438	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.249	125	1438	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	77.9793	148	1438	95	below_threshold
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	77.9636	129	1438	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	77.8615	188	1438	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.5993	200	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:52,267] [INFO] DFAST Taxonomy check result was written to GCF_002499975.2_ASM249997v2_genomic.fna/tc_result.tsv
[2024-01-24 13:55:52,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:52,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:52,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference/checkm_data
[2024-01-24 13:55:52,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:52,317] [INFO] Task started: CheckM
[2024-01-24 13:55:52,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002499975.2_ASM249997v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002499975.2_ASM249997v2_genomic.fna/checkm_input GCF_002499975.2_ASM249997v2_genomic.fna/checkm_result
[2024-01-24 13:56:28,566] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:28,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:28,587] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:28,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:28,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002499975.2_ASM249997v2_genomic.fna/markers.fasta)
[2024-01-24 13:56:28,588] [INFO] Task started: Blastn
[2024-01-24 13:56:28,588] [INFO] Running command: blastn -query GCF_002499975.2_ASM249997v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5be72a7a-5a87-4e7a-9c63-50cf9305c7dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002499975.2_ASM249997v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:29,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:29,459] [INFO] Selected 31 target genomes.
[2024-01-24 13:56:29,459] [INFO] Target genome list was writen to GCF_002499975.2_ASM249997v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:29,501] [INFO] Task started: fastANI
[2024-01-24 13:56:29,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg9904282f-132f-448d-b30a-414cdcc87671/GCF_002499975.2_ASM249997v2_genomic.fna.gz --refList GCF_002499975.2_ASM249997v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002499975.2_ASM249997v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:50,816] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:50,835] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:50,835] [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_002499975.2	s__Alteromonas pelagimontana	100.0	1433	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_001562115.1	s__Alteromonas stellipolaris	78.8508	159	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_014750655.1	s__Alteromonas profundi_A	78.6007	158	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595715.1	s__Glaciecola sp018595715	78.5204	60	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753865.1	s__Alteromonas sp000753865	78.501	115	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002993365.1	s__Alteromonas alba	78.4707	146	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197995.1	s__Aliiglaciecola sp007197995	78.4547	61	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	78.4391	131	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_003429285.1	s__Alteromonas sediminis	78.4312	203	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_010500915.1	s__Alteromonas hispanica	78.3144	137	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCF_006538325.1	s__Alteromonas sp006538325	78.2636	144	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005222225.1	s__Alteromonas lutimaris	78.2545	199	1438	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	78.2516	157	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100795.1	s__Alteromonas sp018100795	78.1768	141	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378185.1	s__Alteromonas chungwhensis	77.9724	149	1438	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367475.1	s__Alteromonas aestuariivivens	77.8615	188	1438	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	77.7457	153	1438	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	77.6464	144	1438	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	77.4336	127	1438	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 13:56:50,837] [INFO] GTDB search result was written to GCF_002499975.2_ASM249997v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:50,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:50,844] [INFO] DFAST_QC result json was written to GCF_002499975.2_ASM249997v2_genomic.fna/dqc_result.json
[2024-01-24 13:56:50,845] [INFO] DFAST_QC completed!
[2024-01-24 13:56:50,845] [INFO] Total running time: 0h1m31s