[2024-01-25 20:02:35,800] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:35,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:35,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference
[2024-01-25 20:02:36,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:36,969] [INFO] Task started: Prodigal
[2024-01-25 20:02:36,969] [INFO] Running command: gunzip -c /var/lib/cwl/stgaedc5140-6ef7-4567-b1a5-9bb4dc78b570/GCF_016584115.1_ASM1658411v1_genomic.fna.gz | prodigal -d GCF_016584115.1_ASM1658411v1_genomic.fna/cds.fna -a GCF_016584115.1_ASM1658411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:44,629] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:44,630] [INFO] Task started: HMMsearch
[2024-01-25 20:02:44,630] [INFO] Running command: hmmsearch --tblout GCF_016584115.1_ASM1658411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference/reference_markers.hmm GCF_016584115.1_ASM1658411v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:44,876] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:44,877] [INFO] Found 6/6 markers.
[2024-01-25 20:02:44,901] [INFO] Query marker FASTA was written to GCF_016584115.1_ASM1658411v1_genomic.fna/markers.fasta
[2024-01-25 20:02:44,901] [INFO] Task started: Blastn
[2024-01-25 20:02:44,902] [INFO] Running command: blastn -query GCF_016584115.1_ASM1658411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference/reference_markers.fasta -out GCF_016584115.1_ASM1658411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:45,776] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:45,778] [INFO] Selected 16 target genomes.
[2024-01-25 20:02:45,779] [INFO] Target genome list was writen to GCF_016584115.1_ASM1658411v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:45,784] [INFO] Task started: fastANI
[2024-01-25 20:02:45,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgaedc5140-6ef7-4567-b1a5-9bb4dc78b570/GCF_016584115.1_ASM1658411v1_genomic.fna.gz --refList GCF_016584115.1_ASM1658411v1_genomic.fna/target_genomes.txt --output GCF_016584115.1_ASM1658411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:56,429] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:56,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:56,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:56,440] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:02:56,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:02:56,440] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	80.4834	423	892	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	80.2278	546	892	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	79.7725	387	892	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	79.2391	326	892	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	79.0916	314	892	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	78.1211	281	892	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.8522	228	892	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	77.6323	211	892	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	77.1264	200	892	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	76.7959	124	892	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.5788	188	892	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5239	183	892	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.3802	222	892	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.289	223	892	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	76.1932	108	892	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.0764	135	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:56,441] [INFO] DFAST Taxonomy check result was written to GCF_016584115.1_ASM1658411v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:56,442] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:56,442] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:56,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference/checkm_data
[2024-01-25 20:02:56,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:56,471] [INFO] Task started: CheckM
[2024-01-25 20:02:56,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016584115.1_ASM1658411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016584115.1_ASM1658411v1_genomic.fna/checkm_input GCF_016584115.1_ASM1658411v1_genomic.fna/checkm_result
[2024-01-25 20:03:27,092] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:27,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:27,114] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:27,114] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:27,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016584115.1_ASM1658411v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:27,115] [INFO] Task started: Blastn
[2024-01-25 20:03:27,115] [INFO] Running command: blastn -query GCF_016584115.1_ASM1658411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg838e052e-7df9-4b0f-8f83-ba6f437880af/dqc_reference/reference_markers_gtdb.fasta -out GCF_016584115.1_ASM1658411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:28,701] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:28,704] [INFO] Selected 10 target genomes.
[2024-01-25 20:03:28,704] [INFO] Target genome list was writen to GCF_016584115.1_ASM1658411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:28,717] [INFO] Task started: fastANI
[2024-01-25 20:03:28,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgaedc5140-6ef7-4567-b1a5-9bb4dc78b570/GCF_016584115.1_ASM1658411v1_genomic.fna.gz --refList GCF_016584115.1_ASM1658411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016584115.1_ASM1658411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:35,264] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:35,272] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:35,272] [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_016584115.1	s__Ectothiorhodospira mobilis	100.0	887	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	93.6341	765	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632845.1	s__Ectothiorhodospira sp001632845	80.9688	533	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.06	99.06	0.98	0.98	2	-
GCF_000633935.1	s__Ectothiorhodospira haloalkaliphila	80.8644	534	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.86	99.86	0.97	0.97	2	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	80.5345	487	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	80.5169	413	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225005.1	s__Ectothiorhodospira sp000225005	80.4678	494	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	80.4648	425	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109495.1	s__Ectothiorhodospira marina	80.2323	546	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488555.1	s__S012-109 sp015488555	77.6236	161	892	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-140;f__SZUA-140;g__S012-109	95.0	99.64	99.60	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:35,274] [INFO] GTDB search result was written to GCF_016584115.1_ASM1658411v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:35,274] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:35,277] [INFO] DFAST_QC result json was written to GCF_016584115.1_ASM1658411v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:35,277] [INFO] DFAST_QC completed!
[2024-01-25 20:03:35,277] [INFO] Total running time: 0h0m59s