[2024-01-24 14:19:15,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,654] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference
[2024-01-24 14:19:18,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,321] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg556a6fff-7524-41d4-90a4-9312a561846a/GCF_004354085.1_ASM435408v1_genomic.fna.gz | prodigal -d GCF_004354085.1_ASM435408v1_genomic.fna/cds.fna -a GCF_004354085.1_ASM435408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:31,312] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:31,312] [INFO] Task started: HMMsearch
[2024-01-24 14:19:31,312] [INFO] Running command: hmmsearch --tblout GCF_004354085.1_ASM435408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference/reference_markers.hmm GCF_004354085.1_ASM435408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:31,647] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:31,648] [INFO] Found 6/6 markers.
[2024-01-24 14:19:31,737] [INFO] Query marker FASTA was written to GCF_004354085.1_ASM435408v1_genomic.fna/markers.fasta
[2024-01-24 14:19:31,737] [INFO] Task started: Blastn
[2024-01-24 14:19:31,737] [INFO] Running command: blastn -query GCF_004354085.1_ASM435408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference/reference_markers.fasta -out GCF_004354085.1_ASM435408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:34,286] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:34,289] [INFO] Selected 14 target genomes.
[2024-01-24 14:19:34,289] [INFO] Target genome list was writen to GCF_004354085.1_ASM435408v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:34,292] [INFO] Task started: fastANI
[2024-01-24 14:19:34,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg556a6fff-7524-41d4-90a4-9312a561846a/GCF_004354085.1_ASM435408v1_genomic.fna.gz --refList GCF_004354085.1_ASM435408v1_genomic.fna/target_genomes.txt --output GCF_004354085.1_ASM435408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:47,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:47,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:47,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:47,947] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:47,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:47,948] [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
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	100.0	1394	1394	95	conclusive
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	82.9004	935	1394	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	78.4676	349	1394	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	78.3328	359	1394	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	78.3311	355	1394	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	78.2713	349	1394	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.2426	386	1394	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	78.2387	374	1394	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.6422	159	1394	95	below_threshold
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	76.6328	73	1394	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	76.5181	93	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:47,950] [INFO] DFAST Taxonomy check result was written to GCF_004354085.1_ASM435408v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:47,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:47,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:47,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference/checkm_data
[2024-01-24 14:19:47,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:48,009] [INFO] Task started: CheckM
[2024-01-24 14:19:48,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354085.1_ASM435408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354085.1_ASM435408v1_genomic.fna/checkm_input GCF_004354085.1_ASM435408v1_genomic.fna/checkm_result
[2024-01-24 14:20:31,442] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:31,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:31,466] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:31,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:31,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354085.1_ASM435408v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:31,467] [INFO] Task started: Blastn
[2024-01-24 14:20:31,467] [INFO] Running command: blastn -query GCF_004354085.1_ASM435408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg759edd90-ef12-4ea0-9d1f-dd15d42886d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354085.1_ASM435408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:33,914] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:33,918] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:33,918] [INFO] Target genome list was writen to GCF_004354085.1_ASM435408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:33,920] [INFO] Task started: fastANI
[2024-01-24 14:20:33,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg556a6fff-7524-41d4-90a4-9312a561846a/GCF_004354085.1_ASM435408v1_genomic.fna.gz --refList GCF_004354085.1_ASM435408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354085.1_ASM435408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:45,570] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:45,640] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:45,641] [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
GCA_004354085.1	s__Halioglobus sp004354085	100.0	1394	1394	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_003457605.1	s__Halioglobus sediminis	82.9004	935	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	78.5765	387	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	78.4573	350	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_008370495.1	s__Halioglobus sp008370495	78.3799	475	1394	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	78.2427	373	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	78.2426	386	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	78.2272	405	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	78.1003	355	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009388985.1	s__Halioglobus maricola	77.9639	340	1394	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	77.8849	374	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_000156295.1	s__Halioglobus sp000156295	77.7425	290	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.94	98.78	0.94	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:45,644] [INFO] GTDB search result was written to GCF_004354085.1_ASM435408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:45,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:45,648] [INFO] DFAST_QC result json was written to GCF_004354085.1_ASM435408v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:45,648] [INFO] DFAST_QC completed!
[2024-01-24 14:20:45,648] [INFO] Total running time: 0h1m30s