[2024-01-25 18:37:20,641] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:20,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:20,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference
[2024-01-25 18:37:21,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:21,760] [INFO] Task started: Prodigal
[2024-01-25 18:37:21,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cd2aa02-9713-4319-ace6-1992dbd1d849/GCF_014077625.1_ASM1407762v1_genomic.fna.gz | prodigal -d GCF_014077625.1_ASM1407762v1_genomic.fna/cds.fna -a GCF_014077625.1_ASM1407762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:29,303] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:29,304] [INFO] Task started: HMMsearch
[2024-01-25 18:37:29,304] [INFO] Running command: hmmsearch --tblout GCF_014077625.1_ASM1407762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference/reference_markers.hmm GCF_014077625.1_ASM1407762v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:29,520] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:29,521] [INFO] Found 6/6 markers.
[2024-01-25 18:37:29,549] [INFO] Query marker FASTA was written to GCF_014077625.1_ASM1407762v1_genomic.fna/markers.fasta
[2024-01-25 18:37:29,550] [INFO] Task started: Blastn
[2024-01-25 18:37:29,550] [INFO] Running command: blastn -query GCF_014077625.1_ASM1407762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference/reference_markers.fasta -out GCF_014077625.1_ASM1407762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:30,207] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:30,210] [INFO] Selected 29 target genomes.
[2024-01-25 18:37:30,210] [INFO] Target genome list was writen to GCF_014077625.1_ASM1407762v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:30,357] [INFO] Task started: fastANI
[2024-01-25 18:37:30,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cd2aa02-9713-4319-ace6-1992dbd1d849/GCF_014077625.1_ASM1407762v1_genomic.fna.gz --refList GCF_014077625.1_ASM1407762v1_genomic.fna/target_genomes.txt --output GCF_014077625.1_ASM1407762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:37:48,234] [INFO] Task succeeded: fastANI
[2024-01-25 18:37:48,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:37:48,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:37:48,248] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:37:48,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:37:48,249] [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
Sediminihaliea albiluteola	strain=F7430	GCA_014077625.1	2758564	2758564	type	True	100.0	1092	1094	95	conclusive
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	77.6379	110	1094	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.6209	175	1094	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.6091	192	1094	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.5992	211	1094	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	77.4108	107	1094	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.3967	105	1094	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.3626	113	1094	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	77.2495	53	1094	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	77.1332	81	1094	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.5998	68	1094	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.5497	71	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:37:48,250] [INFO] DFAST Taxonomy check result was written to GCF_014077625.1_ASM1407762v1_genomic.fna/tc_result.tsv
[2024-01-25 18:37:48,252] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:37:48,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:37:48,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference/checkm_data
[2024-01-25 18:37:48,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:37:48,287] [INFO] Task started: CheckM
[2024-01-25 18:37:48,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014077625.1_ASM1407762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014077625.1_ASM1407762v1_genomic.fna/checkm_input GCF_014077625.1_ASM1407762v1_genomic.fna/checkm_result
[2024-01-25 18:38:14,207] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:14,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:14,225] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:14,226] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:14,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014077625.1_ASM1407762v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:14,227] [INFO] Task started: Blastn
[2024-01-25 18:38:14,227] [INFO] Running command: blastn -query GCF_014077625.1_ASM1407762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82eaca16-55f2-40a0-a472-815513cc9bb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014077625.1_ASM1407762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:15,347] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:15,352] [INFO] Selected 26 target genomes.
[2024-01-25 18:38:15,353] [INFO] Target genome list was writen to GCF_014077625.1_ASM1407762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:15,371] [INFO] Task started: fastANI
[2024-01-25 18:38:15,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cd2aa02-9713-4319-ace6-1992dbd1d849/GCF_014077625.1_ASM1407762v1_genomic.fna.gz --refList GCF_014077625.1_ASM1407762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014077625.1_ASM1407762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:33,182] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:33,190] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:38:33,191] [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_014077625.1	s__Parahaliea sp014077625	100.0	1092	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000158155.1	s__Congregibacter sp000158155	78.0641	72	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Congregibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	77.6255	112	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.6209	175	1094	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	77.6137	210	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.6109	191	1094	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	77.5097	194	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	77.4108	107	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	77.3582	113	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_014652275.1	s__Halioglobus_A pacificus	77.1315	80	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus_A	95.0	98.67	98.67	0.96	0.96	2	-
GCA_002699145.1	s__Halioglobus sp002699145	76.637	81	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_016744355.1	s__Halioglobus sp016744355	76.6263	55	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.6094	69	1094	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:38:33,192] [INFO] GTDB search result was written to GCF_014077625.1_ASM1407762v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:33,192] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:33,197] [INFO] DFAST_QC result json was written to GCF_014077625.1_ASM1407762v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:33,197] [INFO] DFAST_QC completed!
[2024-01-25 18:38:33,197] [INFO] Total running time: 0h1m13s