[2024-01-24 14:14:20,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:20,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:20,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference
[2024-01-24 14:14:21,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,514] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,514] [INFO] Running command: gunzip -c /var/lib/cwl/stga0db53d6-112d-4ee7-a959-68f96eb37c01/GCF_012241385.1_ASM1224138v1_genomic.fna.gz | prodigal -d GCF_012241385.1_ASM1224138v1_genomic.fna/cds.fna -a GCF_012241385.1_ASM1224138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:35,563] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:35,564] [INFO] Task started: HMMsearch
[2024-01-24 14:14:35,564] [INFO] Running command: hmmsearch --tblout GCF_012241385.1_ASM1224138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference/reference_markers.hmm GCF_012241385.1_ASM1224138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:35,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:35,867] [INFO] Found 6/6 markers.
[2024-01-24 14:14:35,911] [INFO] Query marker FASTA was written to GCF_012241385.1_ASM1224138v1_genomic.fna/markers.fasta
[2024-01-24 14:14:35,911] [INFO] Task started: Blastn
[2024-01-24 14:14:35,911] [INFO] Running command: blastn -query GCF_012241385.1_ASM1224138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference/reference_markers.fasta -out GCF_012241385.1_ASM1224138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:36,934] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:36,937] [INFO] Selected 11 target genomes.
[2024-01-24 14:14:36,938] [INFO] Target genome list was writen to GCF_012241385.1_ASM1224138v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:36,944] [INFO] Task started: fastANI
[2024-01-24 14:14:36,944] [INFO] Running command: fastANI --query /var/lib/cwl/stga0db53d6-112d-4ee7-a959-68f96eb37c01/GCF_012241385.1_ASM1224138v1_genomic.fna.gz --refList GCF_012241385.1_ASM1224138v1_genomic.fna/target_genomes.txt --output GCF_012241385.1_ASM1224138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:47,233] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:47,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:47,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:47,244] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:47,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:47,245] [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
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	100.0	1550	1553	95	conclusive
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	82.5812	906	1553	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	82.5572	871	1553	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	82.3239	826	1553	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	82.0652	858	1553	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	79.6781	594	1553	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	77.4612	277	1553	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	76.6417	216	1553	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.5351	198	1553	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	76.3588	263	1553	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.3394	240	1553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:47,246] [INFO] DFAST Taxonomy check result was written to GCF_012241385.1_ASM1224138v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:47,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:47,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:47,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference/checkm_data
[2024-01-24 14:14:47,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:47,295] [INFO] Task started: CheckM
[2024-01-24 14:14:47,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012241385.1_ASM1224138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012241385.1_ASM1224138v1_genomic.fna/checkm_input GCF_012241385.1_ASM1224138v1_genomic.fna/checkm_result
[2024-01-24 14:15:31,727] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:31,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:31,749] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:31,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:31,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012241385.1_ASM1224138v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:31,750] [INFO] Task started: Blastn
[2024-01-24 14:15:31,750] [INFO] Running command: blastn -query GCF_012241385.1_ASM1224138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c20707-411b-47d0-b9d7-8ee6d7e834f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_012241385.1_ASM1224138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:33,602] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:33,605] [INFO] Selected 7 target genomes.
[2024-01-24 14:15:33,605] [INFO] Target genome list was writen to GCF_012241385.1_ASM1224138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:33,611] [INFO] Task started: fastANI
[2024-01-24 14:15:33,611] [INFO] Running command: fastANI --query /var/lib/cwl/stga0db53d6-112d-4ee7-a959-68f96eb37c01/GCF_012241385.1_ASM1224138v1_genomic.fna.gz --refList GCF_012241385.1_ASM1224138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012241385.1_ASM1224138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:40,897] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:40,904] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:40,905] [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_012241385.1	s__Solimonas marina	100.0	1550	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000382285.1	s__Solimonas variicoloris	82.5722	869	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	82.549	910	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	82.3621	821	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	82.0743	857	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	79.6295	601	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	79.3589	558	1553	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,906] [INFO] GTDB search result was written to GCF_012241385.1_ASM1224138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:40,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:40,910] [INFO] DFAST_QC result json was written to GCF_012241385.1_ASM1224138v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:40,910] [INFO] DFAST_QC completed!
[2024-01-24 14:15:40,910] [INFO] Total running time: 0h1m21s