[2024-01-24 13:55:19,898] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference
[2024-01-24 13:55:21,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,310] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg693b4b0e-722b-429a-ab44-24106864a141/GCF_000378185.1_ASM37818v1_genomic.fna.gz | prodigal -d GCF_000378185.1_ASM37818v1_genomic.fna/cds.fna -a GCF_000378185.1_ASM37818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:31,694] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:31,694] [INFO] Task started: HMMsearch
[2024-01-24 13:55:31,694] [INFO] Running command: hmmsearch --tblout GCF_000378185.1_ASM37818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference/reference_markers.hmm GCF_000378185.1_ASM37818v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:32,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:32,034] [INFO] Found 6/6 markers.
[2024-01-24 13:55:32,068] [INFO] Query marker FASTA was written to GCF_000378185.1_ASM37818v1_genomic.fna/markers.fasta
[2024-01-24 13:55:32,069] [INFO] Task started: Blastn
[2024-01-24 13:55:32,069] [INFO] Running command: blastn -query GCF_000378185.1_ASM37818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference/reference_markers.fasta -out GCF_000378185.1_ASM37818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:32,792] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:32,795] [INFO] Selected 19 target genomes.
[2024-01-24 13:55:32,796] [INFO] Target genome list was writen to GCF_000378185.1_ASM37818v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:32,805] [INFO] Task started: fastANI
[2024-01-24 13:55:32,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg693b4b0e-722b-429a-ab44-24106864a141/GCF_000378185.1_ASM37818v1_genomic.fna.gz --refList GCF_000378185.1_ASM37818v1_genomic.fna/target_genomes.txt --output GCF_000378185.1_ASM37818v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:47,289] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:47,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:47,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:47,298] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:47,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:47,299] [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
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	100.0	1312	1314	95	conclusive
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	80.9582	559	1314	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	80.9135	556	1314	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.9195	271	1314	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	77.9195	154	1314	95	below_threshold
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	77.7653	134	1314	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	77.7507	157	1314	95	below_threshold
Alteromonas oceanisediminis	strain=SM 2104	GCA_018474025.1	2836180	2836180	type	True	77.3254	75	1314	95	below_threshold
Lacimicrobium alkaliphilum	strain=X13M-12	GCA_002591895.1	1526571	1526571	type	True	76.8689	63	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:47,300] [INFO] DFAST Taxonomy check result was written to GCF_000378185.1_ASM37818v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:47,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:47,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:47,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference/checkm_data
[2024-01-24 13:55:47,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:47,358] [INFO] Task started: CheckM
[2024-01-24 13:55:47,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378185.1_ASM37818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378185.1_ASM37818v1_genomic.fna/checkm_input GCF_000378185.1_ASM37818v1_genomic.fna/checkm_result
[2024-01-24 13:56:22,140] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:22,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:22,159] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:22,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:22,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378185.1_ASM37818v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:22,160] [INFO] Task started: Blastn
[2024-01-24 13:56:22,160] [INFO] Running command: blastn -query GCF_000378185.1_ASM37818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4daa8b16-1cec-4e72-abfa-f9e45d898c69/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378185.1_ASM37818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:23,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:23,236] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:23,236] [INFO] Target genome list was writen to GCF_000378185.1_ASM37818v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:23,262] [INFO] Task started: fastANI
[2024-01-24 13:56:23,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg693b4b0e-722b-429a-ab44-24106864a141/GCF_000378185.1_ASM37818v1_genomic.fna.gz --refList GCF_000378185.1_ASM37818v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378185.1_ASM37818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:35,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:35,622] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:35,623] [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_000378185.1	s__Alteromonas chungwhensis	100.0	1312	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014750655.1	s__Alteromonas profundi_A	80.952	562	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228385.1	s__Alteromonas iocasae	80.94	557	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	78.9306	269	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	78.8757	264	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_015644725.1	s__Alteromonas sp015644725	78.7046	274	1314	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	78.6834	225	1314	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	78.4051	153	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860965.1	s__Alteromonas sp018860965	78.2579	132	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002499975.2	s__Alteromonas pelagimontana	77.9205	153	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012911815.1	s__Alteromonas ponticola	77.7653	134	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373625.1	s__Alteromonas sp013373625	77.6584	130	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794925.1	s__Alteromonas sp017794925	77.6059	116	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	77.2307	54	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	77.1845	55	1314	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:35,624] [INFO] GTDB search result was written to GCF_000378185.1_ASM37818v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:35,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:35,628] [INFO] DFAST_QC result json was written to GCF_000378185.1_ASM37818v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:35,628] [INFO] DFAST_QC completed!
[2024-01-24 13:56:35,628] [INFO] Total running time: 0h1m16s