[2024-01-24 11:34:41,121] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference
[2024-01-24 11:34:42,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,432] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,432] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f2cf79f-78d3-416c-8aa6-ce30d7530d20/GCF_019430905.1_ASM1943090v1_genomic.fna.gz | prodigal -d GCF_019430905.1_ASM1943090v1_genomic.fna/cds.fna -a GCF_019430905.1_ASM1943090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:56,215] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:56,216] [INFO] Task started: HMMsearch
[2024-01-24 11:34:56,216] [INFO] Running command: hmmsearch --tblout GCF_019430905.1_ASM1943090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference/reference_markers.hmm GCF_019430905.1_ASM1943090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:56,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:56,493] [INFO] Found 6/6 markers.
[2024-01-24 11:34:56,559] [INFO] Query marker FASTA was written to GCF_019430905.1_ASM1943090v1_genomic.fna/markers.fasta
[2024-01-24 11:34:56,560] [INFO] Task started: Blastn
[2024-01-24 11:34:56,560] [INFO] Running command: blastn -query GCF_019430905.1_ASM1943090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference/reference_markers.fasta -out GCF_019430905.1_ASM1943090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:57,596] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:57,599] [INFO] Selected 8 target genomes.
[2024-01-24 11:34:57,600] [INFO] Target genome list was writen to GCF_019430905.1_ASM1943090v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:57,603] [INFO] Task started: fastANI
[2024-01-24 11:34:57,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2cf79f-78d3-416c-8aa6-ce30d7530d20/GCF_019430905.1_ASM1943090v1_genomic.fna.gz --refList GCF_019430905.1_ASM1943090v1_genomic.fna/target_genomes.txt --output GCF_019430905.1_ASM1943090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:06,427] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:06,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:06,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:06,436] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:06,436] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:06,436] [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 antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	100.0	1457	1457	95	inconclusive
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	97.7535	1347	1457	95	inconclusive
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	88.8506	1228	1457	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	87.4414	1163	1457	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	86.8404	1194	1457	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	86.4929	1163	1457	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	86.0978	1027	1457	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	85.2076	1069	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:06,438] [INFO] DFAST Taxonomy check result was written to GCF_019430905.1_ASM1943090v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:06,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:06,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:06,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference/checkm_data
[2024-01-24 11:35:06,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:06,480] [INFO] Task started: CheckM
[2024-01-24 11:35:06,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019430905.1_ASM1943090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019430905.1_ASM1943090v1_genomic.fna/checkm_input GCF_019430905.1_ASM1943090v1_genomic.fna/checkm_result
[2024-01-24 11:35:47,285] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:47,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:47,302] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:47,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:47,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019430905.1_ASM1943090v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:47,303] [INFO] Task started: Blastn
[2024-01-24 11:35:47,303] [INFO] Running command: blastn -query GCF_019430905.1_ASM1943090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg624c4044-ecbb-484f-abcb-0d2d24ce2975/dqc_reference/reference_markers_gtdb.fasta -out GCF_019430905.1_ASM1943090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:49,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:49,042] [INFO] Selected 9 target genomes.
[2024-01-24 11:35:49,043] [INFO] Target genome list was writen to GCF_019430905.1_ASM1943090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:49,049] [INFO] Task started: fastANI
[2024-01-24 11:35:49,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f2cf79f-78d3-416c-8aa6-ce30d7530d20/GCF_019430905.1_ASM1943090v1_genomic.fna.gz --refList GCF_019430905.1_ASM1943090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019430905.1_ASM1943090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:59,102] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,113] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:59,113] [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_017868935.1	s__Halomonas sp017868935	97.7535	1347	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015992245.1	s__Halomonas sp015992245	88.8881	1241	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_003254665.1	s__Halomonas lactosivorans	87.4414	1163	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834345.1	s__Halomonas sp009834345	86.8403	1194	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742165.1	s__Halomonas bachuensis	86.4929	1163	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931605.1	s__Halomonas sp014931605	85.9727	1128	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011742915.1	s__Halomonas desiderata	85.4835	1101	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_000246875.1	s__Halomonas sp000246875	85.3011	1050	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	84.2583	990	1457	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 11:35:59,115] [INFO] GTDB search result was written to GCF_019430905.1_ASM1943090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:59,116] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:59,119] [INFO] DFAST_QC result json was written to GCF_019430905.1_ASM1943090v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:59,119] [INFO] DFAST_QC completed!
[2024-01-24 11:35:59,119] [INFO] Total running time: 0h1m18s