[2024-01-24 13:45:41,640] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:41,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:41,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference
[2024-01-24 13:45:42,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:42,840] [INFO] Task started: Prodigal
[2024-01-24 13:45:42,841] [INFO] Running command: gunzip -c /var/lib/cwl/stge85d4bf1-b22d-4433-b639-ff0500e7d8d9/GCF_013112225.1_ASM1311222v1_genomic.fna.gz | prodigal -d GCF_013112225.1_ASM1311222v1_genomic.fna/cds.fna -a GCF_013112225.1_ASM1311222v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:52,552] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:52,552] [INFO] Task started: HMMsearch
[2024-01-24 13:45:52,552] [INFO] Running command: hmmsearch --tblout GCF_013112225.1_ASM1311222v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference/reference_markers.hmm GCF_013112225.1_ASM1311222v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:52,801] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:52,802] [INFO] Found 6/6 markers.
[2024-01-24 13:45:52,833] [INFO] Query marker FASTA was written to GCF_013112225.1_ASM1311222v1_genomic.fna/markers.fasta
[2024-01-24 13:45:52,833] [INFO] Task started: Blastn
[2024-01-24 13:45:52,833] [INFO] Running command: blastn -query GCF_013112225.1_ASM1311222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference/reference_markers.fasta -out GCF_013112225.1_ASM1311222v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:53,572] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:53,575] [INFO] Selected 24 target genomes.
[2024-01-24 13:45:53,576] [INFO] Target genome list was writen to GCF_013112225.1_ASM1311222v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:53,931] [INFO] Task started: fastANI
[2024-01-24 13:45:53,932] [INFO] Running command: fastANI --query /var/lib/cwl/stge85d4bf1-b22d-4433-b639-ff0500e7d8d9/GCF_013112225.1_ASM1311222v1_genomic.fna.gz --refList GCF_013112225.1_ASM1311222v1_genomic.fna/target_genomes.txt --output GCF_013112225.1_ASM1311222v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:09,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:09,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:09,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:09,947] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:09,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:09,948] [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
Halomonas azerica	strain=TBZ9	GCA_013112225.1	2732867	2732867	type	True	100.0	1128	1130	95	conclusive
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	79.056	371	1130	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	78.9927	370	1130	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	78.9732	308	1130	95	below_threshold
Halomonas subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	78.7616	296	1130	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	78.7113	366	1130	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	78.7052	363	1130	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	78.6211	368	1130	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.6141	282	1130	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	78.5739	297	1130	95	below_threshold
Halomonas salicampi	strain=BH103	GCA_013415105.1	1449798	1449798	type	True	78.5167	346	1130	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	78.3968	325	1130	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	78.3849	305	1130	95	below_threshold
Halomonas zhanjiangensis	strain=DSM 21076	GCA_000377665.1	1121960	1121960	type	True	78.3163	285	1130	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	78.2783	301	1130	95	below_threshold
Halomonas jeotgali	strain=Hwa	GCA_000334215.1	553386	553386	type	True	78.1521	251	1130	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.952	242	1130	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	77.9225	238	1130	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.7649	274	1130	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	77.718	226	1130	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.6678	240	1130	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.4791	242	1130	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	77.4474	262	1130	95	below_threshold
Halomonas saliphila	strain=LCB169	GCA_002930105.1	1848458	1848458	type	True	77.4406	208	1130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:09,951] [INFO] DFAST Taxonomy check result was written to GCF_013112225.1_ASM1311222v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:09,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:09,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:09,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference/checkm_data
[2024-01-24 13:46:09,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:09,991] [INFO] Task started: CheckM
[2024-01-24 13:46:09,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013112225.1_ASM1311222v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013112225.1_ASM1311222v1_genomic.fna/checkm_input GCF_013112225.1_ASM1311222v1_genomic.fna/checkm_result
[2024-01-24 13:46:46,134] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:46,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:46,161] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:46,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:46,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013112225.1_ASM1311222v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:46,162] [INFO] Task started: Blastn
[2024-01-24 13:46:46,163] [INFO] Running command: blastn -query GCF_013112225.1_ASM1311222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5169d0d7-9ad9-486f-b266-4092e03730e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013112225.1_ASM1311222v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:47,511] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:47,514] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:47,514] [INFO] Target genome list was writen to GCF_013112225.1_ASM1311222v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:47,555] [INFO] Task started: fastANI
[2024-01-24 13:46:47,556] [INFO] Running command: fastANI --query /var/lib/cwl/stge85d4bf1-b22d-4433-b639-ff0500e7d8d9/GCF_013112225.1_ASM1311222v1_genomic.fna.gz --refList GCF_013112225.1_ASM1311222v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013112225.1_ASM1311222v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:01,278] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:01,296] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:01,296] [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_013112225.1	s__Halomonas azerica	100.0	1128	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007625055.1	s__Halomonas sp007625055	87.864	699	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813215.1	s__Halomonas sp002813215	81.4268	630	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275725.1	s__Halomonas stevensii	79.0425	371	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_900155385.1	s__Halomonas massiliensis	78.9805	371	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	-
GCF_012427705.1	s__Halomonas piezotolerans	78.9513	311	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_015767635.1	s__Halomonas sp002119345	78.8806	341	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.32	98.32	0.86	0.86	2	-
GCF_900142895.1	s__Halomonas subglaciescola	78.7563	296	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014263395.1	s__Halomonas sp014263395	78.7088	340	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002925.1	s__Halomonas songnenensis	78.7052	363	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	78.7	367	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000686925.1	s__Halomonas sp000686925	78.6867	356	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900110265.1	s__Halomonas aquamarina	78.3985	328	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCA_017983445.1	s__Halomonas sp017983445	78.3396	268	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507855.1	s__Halomonas sp001507855	78.3149	300	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004364445.1	s__Halomonas alkaliantarctica	78.1647	313	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_000334215.1	s__Halomonas jeotgali	78.1512	252	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930105.1	s__Halomonas saliphila	77.4265	209	1130	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:01,303] [INFO] GTDB search result was written to GCF_013112225.1_ASM1311222v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:01,304] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:01,318] [INFO] DFAST_QC result json was written to GCF_013112225.1_ASM1311222v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:01,318] [INFO] DFAST_QC completed!
[2024-01-24 13:47:01,318] [INFO] Total running time: 0h1m20s