[2024-01-24 12:44:54,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:54,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:54,071] [INFO] DQC Reference Directory: /var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference
[2024-01-24 12:44:55,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:55,436] [INFO] Task started: Prodigal
[2024-01-24 12:44:55,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ad818f6-fd77-4859-a4b4-84ac64ccf748/GCF_024199005.1_ASM2419900v1_genomic.fna.gz | prodigal -d GCF_024199005.1_ASM2419900v1_genomic.fna/cds.fna -a GCF_024199005.1_ASM2419900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:02,359] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:02,360] [INFO] Task started: HMMsearch
[2024-01-24 12:45:02,360] [INFO] Running command: hmmsearch --tblout GCF_024199005.1_ASM2419900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference/reference_markers.hmm GCF_024199005.1_ASM2419900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:02,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:02,642] [INFO] Found 6/6 markers.
[2024-01-24 12:45:02,682] [INFO] Query marker FASTA was written to GCF_024199005.1_ASM2419900v1_genomic.fna/markers.fasta
[2024-01-24 12:45:02,683] [INFO] Task started: Blastn
[2024-01-24 12:45:02,683] [INFO] Running command: blastn -query GCF_024199005.1_ASM2419900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference/reference_markers.fasta -out GCF_024199005.1_ASM2419900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:03,448] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:03,451] [INFO] Selected 34 target genomes.
[2024-01-24 12:45:03,452] [INFO] Target genome list was writen to GCF_024199005.1_ASM2419900v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:03,470] [INFO] Task started: fastANI
[2024-01-24 12:45:03,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad818f6-fd77-4859-a4b4-84ac64ccf748/GCF_024199005.1_ASM2419900v1_genomic.fna.gz --refList GCF_024199005.1_ASM2419900v1_genomic.fna/target_genomes.txt --output GCF_024199005.1_ASM2419900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:23,300] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:23,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:23,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:23,317] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:23,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:23,317] [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 hispanica	strain=LMG 22958	GCA_010500915.1	315421	315421	type	True	78.7134	56	923	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.3313	59	923	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	77.9971	57	923	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	77.9875	58	923	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	77.9402	60	923	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.7775	64	923	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	77.7115	62	923	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.7113	55	923	95	below_threshold
Ningiella ruwaisensis	strain=B66	GCA_004798935.1	2364274	2364274	type	True	77.5899	50	923	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	77.4991	54	923	95	below_threshold
Marinifaba aquimaris	strain=SM1970	GCA_013328345.1	2741323	2741323	type	True	77.2523	52	923	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:23,320] [INFO] DFAST Taxonomy check result was written to GCF_024199005.1_ASM2419900v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:23,321] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:23,321] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:23,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference/checkm_data
[2024-01-24 12:45:23,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:23,355] [INFO] Task started: CheckM
[2024-01-24 12:45:23,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024199005.1_ASM2419900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024199005.1_ASM2419900v1_genomic.fna/checkm_input GCF_024199005.1_ASM2419900v1_genomic.fna/checkm_result
[2024-01-24 12:45:49,629] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:49,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:49,655] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:49,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:49,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024199005.1_ASM2419900v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:49,656] [INFO] Task started: Blastn
[2024-01-24 12:45:49,656] [INFO] Running command: blastn -query GCF_024199005.1_ASM2419900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg757176ab-32a5-448a-a31f-7864890356eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_024199005.1_ASM2419900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:50,815] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:50,820] [INFO] Selected 29 target genomes.
[2024-01-24 12:45:50,821] [INFO] Target genome list was writen to GCF_024199005.1_ASM2419900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:50,843] [INFO] Task started: fastANI
[2024-01-24 12:45:50,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ad818f6-fd77-4859-a4b4-84ac64ccf748/GCF_024199005.1_ASM2419900v1_genomic.fna.gz --refList GCF_024199005.1_ASM2419900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024199005.1_ASM2419900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:07,426] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:07,453] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:07,454] [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_000155775.1	s__Glaciecola sp000155775	78.4778	150	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	78.4596	63	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_001953635.1	s__Alteromonas abrolhosensis	78.3548	58	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_003203515.1	s__Glaciecola sp003203515	78.3289	70	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885075.1	s__Alteromonas sp001885075	78.3236	58	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872805.1	s__Glaciecola sp014872805	78.0857	114	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	78.0496	58	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	78.0052	65	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314975.1	s__Aliiglaciecola lipolytica	77.979	58	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	77.9684	60	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCA_018623155.1	s__Glaciecola sp018623155	77.9399	117	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	77.8787	52	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292215.1	s__Glaciecola sp002292215	77.8756	150	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	-
GCF_018861065.1	s__Paraglaciecola arctica_B	77.8411	66	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538325.1	s__Alteromonas sp006538325	77.8154	72	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005117025.1	s__Alteromonas portus	77.7236	61	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811415.1	s__Alteromonas sp009811415	77.6838	51	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	77.6271	63	923	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373625.1	s__Alteromonas sp013373625	77.1935	62	923	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 12:46:07,455] [INFO] GTDB search result was written to GCF_024199005.1_ASM2419900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:07,456] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:07,460] [INFO] DFAST_QC result json was written to GCF_024199005.1_ASM2419900v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:07,460] [INFO] DFAST_QC completed!
[2024-01-24 12:46:07,460] [INFO] Total running time: 0h1m13s