[2024-01-25 19:05:35,632] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:35,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:35,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference
[2024-01-25 19:05:36,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:36,772] [INFO] Task started: Prodigal
[2024-01-25 19:05:36,772] [INFO] Running command: gunzip -c /var/lib/cwl/stgc149425b-b97f-4f47-9268-e3bbc3562309/GCF_014652275.1_ASM1465227v1_genomic.fna.gz | prodigal -d GCF_014652275.1_ASM1465227v1_genomic.fna/cds.fna -a GCF_014652275.1_ASM1465227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:46,528] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:46,528] [INFO] Task started: HMMsearch
[2024-01-25 19:05:46,528] [INFO] Running command: hmmsearch --tblout GCF_014652275.1_ASM1465227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference/reference_markers.hmm GCF_014652275.1_ASM1465227v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:46,734] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:46,735] [INFO] Found 6/6 markers.
[2024-01-25 19:05:46,763] [INFO] Query marker FASTA was written to GCF_014652275.1_ASM1465227v1_genomic.fna/markers.fasta
[2024-01-25 19:05:46,764] [INFO] Task started: Blastn
[2024-01-25 19:05:46,764] [INFO] Running command: blastn -query GCF_014652275.1_ASM1465227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference/reference_markers.fasta -out GCF_014652275.1_ASM1465227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:47,455] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:47,457] [INFO] Selected 25 target genomes.
[2024-01-25 19:05:47,458] [INFO] Target genome list was writen to GCF_014652275.1_ASM1465227v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:47,477] [INFO] Task started: fastANI
[2024-01-25 19:05:47,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgc149425b-b97f-4f47-9268-e3bbc3562309/GCF_014652275.1_ASM1465227v1_genomic.fna.gz --refList GCF_014652275.1_ASM1465227v1_genomic.fna/target_genomes.txt --output GCF_014652275.1_ASM1465227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:03,507] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:03,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:03,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:03,517] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:06:03,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:03,517] [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 pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	100.0	1136	1136	95	conclusive
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.8159	169	1136	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.8061	168	1136	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.806	171	1136	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.1712	193	1136	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.1003	178	1136	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.984	184	1136	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.9731	222	1136	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	76.9206	135	1136	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.9004	134	1136	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.4651	95	1136	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.8092	59	1136	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.5364	51	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:03,521] [INFO] DFAST Taxonomy check result was written to GCF_014652275.1_ASM1465227v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:03,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:03,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:03,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference/checkm_data
[2024-01-25 19:06:03,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:03,560] [INFO] Task started: CheckM
[2024-01-25 19:06:03,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652275.1_ASM1465227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652275.1_ASM1465227v1_genomic.fna/checkm_input GCF_014652275.1_ASM1465227v1_genomic.fna/checkm_result
[2024-01-25 19:06:35,149] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:35,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:35,193] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:35,193] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:35,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652275.1_ASM1465227v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:35,194] [INFO] Task started: Blastn
[2024-01-25 19:06:35,194] [INFO] Running command: blastn -query GCF_014652275.1_ASM1465227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca6805b4-13a4-4093-bf1e-6874ce07c31c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652275.1_ASM1465227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:36,385] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:36,388] [INFO] Selected 22 target genomes.
[2024-01-25 19:06:36,388] [INFO] Target genome list was writen to GCF_014652275.1_ASM1465227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:36,418] [INFO] Task started: fastANI
[2024-01-25 19:06:36,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgc149425b-b97f-4f47-9268-e3bbc3562309/GCF_014652275.1_ASM1465227v1_genomic.fna.gz --refList GCF_014652275.1_ASM1465227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652275.1_ASM1465227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:50,520] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:50,530] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:50,530] [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_014652275.1	s__Halioglobus_A pacificus	100.0	1136	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus_A	95.0	98.67	98.67	0.96	0.96	2	conclusive
GCF_001983995.1	s__Halioglobus japonicus	77.806	171	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_004745945.1	s__Halioglobus sp004745945	77.2538	144	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.2443	192	1136	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	77.1712	193	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.1003	178	1136	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	77.0519	142	1136	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	76.9849	221	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.984	184	1136	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	76.9004	134	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	76.8789	146	1136	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	76.7014	97	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002868715.1	s__Kineobactrum sediminis	76.4646	94	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646405.1	s__Halioglobus sp003646405	76.1059	83	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:50,531] [INFO] GTDB search result was written to GCF_014652275.1_ASM1465227v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:50,532] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:50,535] [INFO] DFAST_QC result json was written to GCF_014652275.1_ASM1465227v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:50,535] [INFO] DFAST_QC completed!
[2024-01-25 19:06:50,535] [INFO] Total running time: 0h1m15s