[2024-01-25 18:09:35,982] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:35,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:35,990] [INFO] DQC Reference Directory: /var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference
[2024-01-25 18:09:37,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:37,277] [INFO] Task started: Prodigal
[2024-01-25 18:09:37,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg61e7fa25-7b19-4b61-b5ea-fff3699dae67/GCF_028595265.1_ASM2859526v1_genomic.fna.gz | prodigal -d GCF_028595265.1_ASM2859526v1_genomic.fna/cds.fna -a GCF_028595265.1_ASM2859526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:47,523] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:47,523] [INFO] Task started: HMMsearch
[2024-01-25 18:09:47,524] [INFO] Running command: hmmsearch --tblout GCF_028595265.1_ASM2859526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference/reference_markers.hmm GCF_028595265.1_ASM2859526v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:47,758] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:47,759] [INFO] Found 6/6 markers.
[2024-01-25 18:09:47,797] [INFO] Query marker FASTA was written to GCF_028595265.1_ASM2859526v1_genomic.fna/markers.fasta
[2024-01-25 18:09:47,798] [INFO] Task started: Blastn
[2024-01-25 18:09:47,798] [INFO] Running command: blastn -query GCF_028595265.1_ASM2859526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference/reference_markers.fasta -out GCF_028595265.1_ASM2859526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:48,485] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:48,488] [INFO] Selected 22 target genomes.
[2024-01-25 18:09:48,488] [INFO] Target genome list was writen to GCF_028595265.1_ASM2859526v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:48,512] [INFO] Task started: fastANI
[2024-01-25 18:09:48,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg61e7fa25-7b19-4b61-b5ea-fff3699dae67/GCF_028595265.1_ASM2859526v1_genomic.fna.gz --refList GCF_028595265.1_ASM2859526v1_genomic.fna/target_genomes.txt --output GCF_028595265.1_ASM2859526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:05,446] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:05,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:05,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:05,458] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:10:05,458] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:10:05,459] [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 alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	79.4726	510	1521	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	79.3769	519	1521	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	79.1236	478	1521	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	79.0857	469	1521	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.8101	149	1521	95	below_threshold
Alteromonas hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.5292	114	1521	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	78.5204	121	1521	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.4515	156	1521	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	78.437	138	1521	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	78.3197	115	1521	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.2894	134	1521	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.1683	121	1521	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.0889	180	1521	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	77.8428	187	1521	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	77.8307	140	1521	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.7377	66	1521	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	76.89	71	1521	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	75.9799	71	1521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:05,460] [INFO] DFAST Taxonomy check result was written to GCF_028595265.1_ASM2859526v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:05,460] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:05,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:05,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference/checkm_data
[2024-01-25 18:10:05,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:05,505] [INFO] Task started: CheckM
[2024-01-25 18:10:05,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028595265.1_ASM2859526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028595265.1_ASM2859526v1_genomic.fna/checkm_input GCF_028595265.1_ASM2859526v1_genomic.fna/checkm_result
[2024-01-25 18:10:38,571] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:38,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:38,632] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:38,632] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:38,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028595265.1_ASM2859526v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:38,633] [INFO] Task started: Blastn
[2024-01-25 18:10:38,633] [INFO] Running command: blastn -query GCF_028595265.1_ASM2859526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc285341c-cadb-4587-8f36-4c357ce6c1b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_028595265.1_ASM2859526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:39,708] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:39,711] [INFO] Selected 8 target genomes.
[2024-01-25 18:10:39,711] [INFO] Target genome list was writen to GCF_028595265.1_ASM2859526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:39,719] [INFO] Task started: fastANI
[2024-01-25 18:10:39,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg61e7fa25-7b19-4b61-b5ea-fff3699dae67/GCF_028595265.1_ASM2859526v1_genomic.fna.gz --refList GCF_028595265.1_ASM2859526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028595265.1_ASM2859526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:46,705] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:46,711] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:10:46,711] [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
GCA_013373625.1	s__Alteromonas sp013373625	82.2999	977	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	79.4627	511	1521	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	79.4125	415	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.62	99.31	0.91	0.90	3	-
GCF_003731635.1	s__Alteromonas oceani	79.4063	517	1521	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	79.2731	516	1521	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	79.2598	487	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
GCF_001758465.1	s__Alteromonas lipolytica	79.1331	477	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000597705.1	s__Alteromonas sp000597705	78.2247	143	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:46,713] [INFO] GTDB search result was written to GCF_028595265.1_ASM2859526v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:46,719] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:46,722] [INFO] DFAST_QC result json was written to GCF_028595265.1_ASM2859526v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:46,722] [INFO] DFAST_QC completed!
[2024-01-25 18:10:46,722] [INFO] Total running time: 0h1m11s