[2024-01-24 13:46:18,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference
[2024-01-24 13:46:19,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,699] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg67102909-eff4-47ed-af89-1a0057fbea4c/GCF_000213655.1_ASM21365v1_genomic.fna.gz | prodigal -d GCF_000213655.1_ASM21365v1_genomic.fna/cds.fna -a GCF_000213655.1_ASM21365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:31,755] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:31,756] [INFO] Task started: HMMsearch
[2024-01-24 13:46:31,756] [INFO] Running command: hmmsearch --tblout GCF_000213655.1_ASM21365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference/reference_markers.hmm GCF_000213655.1_ASM21365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:32,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:32,097] [INFO] Found 6/6 markers.
[2024-01-24 13:46:32,149] [INFO] Query marker FASTA was written to GCF_000213655.1_ASM21365v1_genomic.fna/markers.fasta
[2024-01-24 13:46:32,149] [INFO] Task started: Blastn
[2024-01-24 13:46:32,150] [INFO] Running command: blastn -query GCF_000213655.1_ASM21365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference/reference_markers.fasta -out GCF_000213655.1_ASM21365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:32,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:32,915] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:32,915] [INFO] Target genome list was writen to GCF_000213655.1_ASM21365v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:32,923] [INFO] Task started: fastANI
[2024-01-24 13:46:32,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg67102909-eff4-47ed-af89-1a0057fbea4c/GCF_000213655.1_ASM21365v1_genomic.fna.gz --refList GCF_000213655.1_ASM21365v1_genomic.fna/target_genomes.txt --output GCF_000213655.1_ASM21365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:48,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:48,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:48,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:48,481] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:48,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:48,481] [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 naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	100.0	1657	1657	95	conclusive
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	93.0118	1285	1657	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	80.1934	427	1657	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	79.7017	460	1657	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	79.671	384	1657	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	79.5445	465	1657	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	79.5044	427	1657	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	79.4685	422	1657	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	79.2511	339	1657	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	79.0422	430	1657	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	78.8537	64	1657	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.8339	53	1657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:48,483] [INFO] DFAST Taxonomy check result was written to GCF_000213655.1_ASM21365v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:48,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:48,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:48,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference/checkm_data
[2024-01-24 13:46:48,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:48,546] [INFO] Task started: CheckM
[2024-01-24 13:46:48,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000213655.1_ASM21365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000213655.1_ASM21365v1_genomic.fna/checkm_input GCF_000213655.1_ASM21365v1_genomic.fna/checkm_result
[2024-01-24 13:47:27,949] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:27,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:27,972] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:27,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:27,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000213655.1_ASM21365v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:27,973] [INFO] Task started: Blastn
[2024-01-24 13:47:27,973] [INFO] Running command: blastn -query GCF_000213655.1_ASM21365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3af7845-815a-4008-9aa7-bbf2eeedc5d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000213655.1_ASM21365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:29,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:29,150] [INFO] Selected 8 target genomes.
[2024-01-24 13:47:29,150] [INFO] Target genome list was writen to GCF_000213655.1_ASM21365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:29,161] [INFO] Task started: fastANI
[2024-01-24 13:47:29,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg67102909-eff4-47ed-af89-1a0057fbea4c/GCF_000213655.1_ASM21365v1_genomic.fna.gz --refList GCF_000213655.1_ASM21365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000213655.1_ASM21365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:37,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:38,011] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:38,012] [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_000213655.1	s__Alteromonas naphthalenivorans	100.0	1657	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	conclusive
GCF_902506055.1	s__Alteromonas lipotrueae	93.0317	1296	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCA_001562115.1	s__Alteromonas stellipolaris	90.623	1338	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_018100795.1	s__Alteromonas sp018100795	90.3011	1267	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405965.1	s__Alteromonas sp016405965	79.7341	422	1657	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	79.6795	462	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730385.1	s__Alteromonas australica	79.5761	465	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.80	98.45	0.91	0.74	29	-
GCF_006538325.1	s__Alteromonas sp006538325	79.1967	351	1657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:38,013] [INFO] GTDB search result was written to GCF_000213655.1_ASM21365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:38,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:38,017] [INFO] DFAST_QC result json was written to GCF_000213655.1_ASM21365v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:38,017] [INFO] DFAST_QC completed!
[2024-01-24 13:47:38,017] [INFO] Total running time: 0h1m20s