[2024-01-24 13:46:16,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:16,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:16,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference
[2024-01-24 13:46:18,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:18,046] [INFO] Task started: Prodigal
[2024-01-24 13:46:18,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg6783ca6c-160a-4a1d-8166-5cab39ed45f9/GCF_000013045.1_ASM1304v1_genomic.fna.gz | prodigal -d GCF_000013045.1_ASM1304v1_genomic.fna/cds.fna -a GCF_000013045.1_ASM1304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:41,149] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:41,150] [INFO] Task started: HMMsearch
[2024-01-24 13:46:41,150] [INFO] Running command: hmmsearch --tblout GCF_000013045.1_ASM1304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference/reference_markers.hmm GCF_000013045.1_ASM1304v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:41,430] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:41,431] [INFO] Found 6/6 markers.
[2024-01-24 13:46:41,463] [INFO] Query marker FASTA was written to GCF_000013045.1_ASM1304v1_genomic.fna/markers.fasta
[2024-01-24 13:46:41,463] [INFO] Task started: Blastn
[2024-01-24 13:46:41,463] [INFO] Running command: blastn -query GCF_000013045.1_ASM1304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference/reference_markers.fasta -out GCF_000013045.1_ASM1304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:42,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:42,180] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:42,180] [INFO] Target genome list was writen to GCF_000013045.1_ASM1304v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:42,196] [INFO] Task started: fastANI
[2024-01-24 13:46:42,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg6783ca6c-160a-4a1d-8166-5cab39ed45f9/GCF_000013045.1_ASM1304v1_genomic.fna.gz --refList GCF_000013045.1_ASM1304v1_genomic.fna/target_genomes.txt --output GCF_000013045.1_ASM1304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:54,600] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:54,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:54,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:54,611] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:54,612] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:54,612] [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
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	100.0	1194	1194	95	conclusive
Salinibacter altiplanensis	strain=AN15	GCA_002894645.1	1803181	1803181	type	True	85.0965	875	1194	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	76.8391	155	1194	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.5369	145	1194	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	76.5116	114	1194	95	below_threshold
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	76.4845	124	1194	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	75.8775	128	1194	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	75.082	51	1194	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	75.066	51	1194	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.0516	52	1194	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.9567	62	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:54,614] [INFO] DFAST Taxonomy check result was written to GCF_000013045.1_ASM1304v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:54,614] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:54,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:54,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference/checkm_data
[2024-01-24 13:46:54,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:54,662] [INFO] Task started: CheckM
[2024-01-24 13:46:54,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013045.1_ASM1304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013045.1_ASM1304v1_genomic.fna/checkm_input GCF_000013045.1_ASM1304v1_genomic.fna/checkm_result
[2024-01-24 13:47:52,966] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:52,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:52,985] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:52,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:52,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013045.1_ASM1304v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:52,987] [INFO] Task started: Blastn
[2024-01-24 13:47:52,987] [INFO] Running command: blastn -query GCF_000013045.1_ASM1304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cdb1e4c-4378-4e73-806c-b7155bf9633b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013045.1_ASM1304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:53,939] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:53,942] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:53,943] [INFO] Target genome list was writen to GCF_000013045.1_ASM1304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:53,966] [INFO] Task started: fastANI
[2024-01-24 13:47:53,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg6783ca6c-160a-4a1d-8166-5cab39ed45f9/GCF_000013045.1_ASM1304v1_genomic.fna.gz --refList GCF_000013045.1_ASM1304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013045.1_ASM1304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:00,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:00,469] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:00,469] [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_000013045.1	s__Salinibacter ruber	100.0	1194	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.51	97.79	0.92	0.85	14	conclusive
GCF_002894645.1	s__Salinibacter altiplanensis	85.0726	877	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	98.33	98.12	0.91	0.90	3	-
GCA_003023105.1	s__Salinibacter sp003023105	80.7683	275	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022565.1	s__Salinibacter sp003022565	80.7223	505	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022655.1	s__Salinibacter sp003022655	80.6731	330	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002894685.1	s__Salinibacter luteus	79.6193	487	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCF_002894665.1	s__Salinibacter iranicus	79.5372	479	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	96.2585	N/A	N/A	N/A	N/A	1	-
GCA_003023125.1	s__Salinibacter sp003023125	79.3754	235	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	95.78	95.78	0.67	0.67	2	-
GCA_003022435.1	s__Salinibacter sp003022435	78.4391	310	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023365.1	s__Salinibacter sp003023365	77.8724	216	1194	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__Salinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:00,471] [INFO] GTDB search result was written to GCF_000013045.1_ASM1304v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:00,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:00,476] [INFO] DFAST_QC result json was written to GCF_000013045.1_ASM1304v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:00,477] [INFO] DFAST_QC completed!
[2024-01-24 13:48:00,477] [INFO] Total running time: 0h1m44s