[2024-01-24 14:47:55,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference
[2024-01-24 14:47:58,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,520] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgba2dafeb-3068-46eb-9260-2f270496d14c/GCF_009388985.1_ASM938898v1_genomic.fna.gz | prodigal -d GCF_009388985.1_ASM938898v1_genomic.fna/cds.fna -a GCF_009388985.1_ASM938898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:11,578] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:11,578] [INFO] Task started: HMMsearch
[2024-01-24 14:48:11,579] [INFO] Running command: hmmsearch --tblout GCF_009388985.1_ASM938898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference/reference_markers.hmm GCF_009388985.1_ASM938898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:11,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:11,877] [INFO] Found 6/6 markers.
[2024-01-24 14:48:11,922] [INFO] Query marker FASTA was written to GCF_009388985.1_ASM938898v1_genomic.fna/markers.fasta
[2024-01-24 14:48:11,922] [INFO] Task started: Blastn
[2024-01-24 14:48:11,923] [INFO] Running command: blastn -query GCF_009388985.1_ASM938898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference/reference_markers.fasta -out GCF_009388985.1_ASM938898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:12,716] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:12,720] [INFO] Selected 17 target genomes.
[2024-01-24 14:48:12,721] [INFO] Target genome list was writen to GCF_009388985.1_ASM938898v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:12,737] [INFO] Task started: fastANI
[2024-01-24 14:48:12,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgba2dafeb-3068-46eb-9260-2f270496d14c/GCF_009388985.1_ASM938898v1_genomic.fna.gz --refList GCF_009388985.1_ASM938898v1_genomic.fna/target_genomes.txt --output GCF_009388985.1_ASM938898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:25,627] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:25,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:25,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:25,645] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:25,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:25,645] [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
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	100.0	1435	1435	95	conclusive
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	79.5505	546	1435	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	79.4211	551	1435	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	79.4044	550	1435	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.0725	330	1435	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.0448	349	1435	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.582	235	1435	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.4872	239	1435	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	76.9412	77	1435	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	76.8173	59	1435	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	76.6381	56	1435	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	76.5449	54	1435	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.4983	50	1435	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	76.446	67	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:25,648] [INFO] DFAST Taxonomy check result was written to GCF_009388985.1_ASM938898v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:25,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:25,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:25,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference/checkm_data
[2024-01-24 14:48:25,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:25,688] [INFO] Task started: CheckM
[2024-01-24 14:48:25,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009388985.1_ASM938898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009388985.1_ASM938898v1_genomic.fna/checkm_input GCF_009388985.1_ASM938898v1_genomic.fna/checkm_result
[2024-01-24 14:49:07,223] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:07,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:07,247] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:07,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:07,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009388985.1_ASM938898v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:07,249] [INFO] Task started: Blastn
[2024-01-24 14:49:07,249] [INFO] Running command: blastn -query GCF_009388985.1_ASM938898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93aeddc7-1728-49ac-a1ec-884527243dfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_009388985.1_ASM938898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:08,560] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:08,564] [INFO] Selected 14 target genomes.
[2024-01-24 14:49:08,564] [INFO] Target genome list was writen to GCF_009388985.1_ASM938898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:08,575] [INFO] Task started: fastANI
[2024-01-24 14:49:08,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgba2dafeb-3068-46eb-9260-2f270496d14c/GCF_009388985.1_ASM938898v1_genomic.fna.gz --refList GCF_009388985.1_ASM938898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009388985.1_ASM938898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:20,587] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:20,610] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:20,611] [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_009388985.1	s__Halioglobus maricola	100.0	1435	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001983995.1	s__Halioglobus japonicus	79.5519	545	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_004354085.1	s__Halioglobus sp004354085	78.083	329	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	78.0448	349	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.6285	201	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.5957	234	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	77.5701	243	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCF_004745945.1	s__Halioglobus sp004745945	77.5023	263	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.4872	239	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.4524	301	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.8823	226	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_002868715.1	s__Kineobactrum sediminis	76.6309	133	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106015.1	s__Pseudomonas_E sihuiensis	76.6175	68	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_013385425.1	s__Pseudomonas_E gingeri_D	76.0644	57	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.70	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:20,613] [INFO] GTDB search result was written to GCF_009388985.1_ASM938898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:20,613] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:20,618] [INFO] DFAST_QC result json was written to GCF_009388985.1_ASM938898v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:20,618] [INFO] DFAST_QC completed!
[2024-01-24 14:49:20,618] [INFO] Total running time: 0h1m25s