[2024-01-24 15:26:04,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a090216-24ec-46c3-ae83-00bd9b6ecfa2/GCF_004340525.1_ASM434052v1_genomic.fna.gz | prodigal -d GCF_004340525.1_ASM434052v1_genomic.fna/cds.fna -a GCF_004340525.1_ASM434052v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:18,756] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:18,757] [INFO] Task started: HMMsearch
[2024-01-24 15:26:18,757] [INFO] Running command: hmmsearch --tblout GCF_004340525.1_ASM434052v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference/reference_markers.hmm GCF_004340525.1_ASM434052v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:19,058] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:19,059] [INFO] Found 6/6 markers.
[2024-01-24 15:26:19,096] [INFO] Query marker FASTA was written to GCF_004340525.1_ASM434052v1_genomic.fna/markers.fasta
[2024-01-24 15:26:19,096] [INFO] Task started: Blastn
[2024-01-24 15:26:19,096] [INFO] Running command: blastn -query GCF_004340525.1_ASM434052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference/reference_markers.fasta -out GCF_004340525.1_ASM434052v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:19,916] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:19,923] [INFO] Selected 17 target genomes.
[2024-01-24 15:26:19,924] [INFO] Target genome list was writen to GCF_004340525.1_ASM434052v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:19,932] [INFO] Task started: fastANI
[2024-01-24 15:26:19,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a090216-24ec-46c3-ae83-00bd9b6ecfa2/GCF_004340525.1_ASM434052v1_genomic.fna.gz --refList GCF_004340525.1_ASM434052v1_genomic.fna/target_genomes.txt --output GCF_004340525.1_ASM434052v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:32,302] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:32,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:32,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:32,322] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:26:32,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:32,322] [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
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	100.0	1276	1279	95	conclusive
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	99.98	1260	1279	95	conclusive
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	77.6094	267	1279	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.4523	217	1279	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.3311	199	1279	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.2972	241	1279	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.2711	204	1279	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.0413	206	1279	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.0002	151	1279	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.7001	97	1279	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5445	109	1279	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.4846	120	1279	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.399	123	1279	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.3756	103	1279	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.1688	98	1279	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.1204	98	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:32,324] [INFO] DFAST Taxonomy check result was written to GCF_004340525.1_ASM434052v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:32,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:32,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:32,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference/checkm_data
[2024-01-24 15:26:32,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:32,373] [INFO] Task started: CheckM
[2024-01-24 15:26:32,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340525.1_ASM434052v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340525.1_ASM434052v1_genomic.fna/checkm_input GCF_004340525.1_ASM434052v1_genomic.fna/checkm_result
[2024-01-24 15:27:10,433] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:10,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:10,454] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:10,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:10,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340525.1_ASM434052v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:10,456] [INFO] Task started: Blastn
[2024-01-24 15:27:10,456] [INFO] Running command: blastn -query GCF_004340525.1_ASM434052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b6300ba-482e-4e71-b856-19a896420d69/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340525.1_ASM434052v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:11,882] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:11,887] [INFO] Selected 20 target genomes.
[2024-01-24 15:27:11,888] [INFO] Target genome list was writen to GCF_004340525.1_ASM434052v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:11,906] [INFO] Task started: fastANI
[2024-01-24 15:27:11,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a090216-24ec-46c3-ae83-00bd9b6ecfa2/GCF_004340525.1_ASM434052v1_genomic.fna.gz --refList GCF_004340525.1_ASM434052v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340525.1_ASM434052v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:26,285] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:26,303] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:26,304] [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_004340525.1	s__Chromatocurvus halotolerans	100.0	1276	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_017255185.1	s__Parahaliea mediterranea_A	77.6306	258	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764025.1	s__Pseudohaliea rubra	77.5991	268	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.4523	217	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	77.3459	198	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003402235.1	s__Parahaliea mediterranea	77.2972	241	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.2711	243	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	77.0523	222	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_002699145.1	s__Halioglobus sp002699145	77.0352	229	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_003457605.1	s__Halioglobus sediminis	77.0283	207	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	77.017	150	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.8619	159	1279	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	76.8045	176	1279	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	76.7001	97	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	76.6568	205	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_001983995.1	s__Halioglobus japonicus	76.4846	120	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.2784	119	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.1835	104	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.1405	86	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:26,305] [INFO] GTDB search result was written to GCF_004340525.1_ASM434052v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:26,306] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:26,312] [INFO] DFAST_QC result json was written to GCF_004340525.1_ASM434052v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:26,312] [INFO] DFAST_QC completed!
[2024-01-24 15:27:26,312] [INFO] Total running time: 0h1m22s