[2024-01-25 19:50:35,360] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:35,361] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:35,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference
[2024-01-25 19:50:36,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:36,519] [INFO] Task started: Prodigal
[2024-01-25 19:50:36,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg2da37e8e-9b3f-41c5-8bd9-a1381587ce39/GCF_001922575.1_ASM192257v1_genomic.fna.gz | prodigal -d GCF_001922575.1_ASM192257v1_genomic.fna/cds.fna -a GCF_001922575.1_ASM192257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:44,278] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:44,279] [INFO] Task started: HMMsearch
[2024-01-25 19:50:44,279] [INFO] Running command: hmmsearch --tblout GCF_001922575.1_ASM192257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference/reference_markers.hmm GCF_001922575.1_ASM192257v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:44,503] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:44,504] [INFO] Found 6/6 markers.
[2024-01-25 19:50:44,534] [INFO] Query marker FASTA was written to GCF_001922575.1_ASM192257v1_genomic.fna/markers.fasta
[2024-01-25 19:50:44,535] [INFO] Task started: Blastn
[2024-01-25 19:50:44,535] [INFO] Running command: blastn -query GCF_001922575.1_ASM192257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference/reference_markers.fasta -out GCF_001922575.1_ASM192257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:45,134] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:45,136] [INFO] Selected 29 target genomes.
[2024-01-25 19:50:45,137] [INFO] Target genome list was writen to GCF_001922575.1_ASM192257v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:45,169] [INFO] Task started: fastANI
[2024-01-25 19:50:45,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da37e8e-9b3f-41c5-8bd9-a1381587ce39/GCF_001922575.1_ASM192257v1_genomic.fna.gz --refList GCF_001922575.1_ASM192257v1_genomic.fna/target_genomes.txt --output GCF_001922575.1_ASM192257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:01,657] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:01,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:01,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:01,665] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:01,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:01,665] [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
Neptunomonas phycophila	strain=CECT 8716	GCA_001922575.1	1572645	1572645	type	True	100.0	1281	1284	95	conclusive
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	78.9752	137	1284	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	78.4309	134	1284	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	77.7878	69	1284	95	below_threshold
Neptunomonas japonica	strain=DSM 18939	GCA_000422765.1	417574	417574	type	True	77.7731	133	1284	95	below_threshold
Neptunomonas antarctica	strain=DSM 22306	GCA_900156635.1	619304	619304	type	True	77.742	118	1284	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	77.5787	72	1284	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	77.5421	126	1284	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	77.5078	124	1284	95	below_threshold
Neptunomonas antarctica	strain=S3-22	GCA_001305295.1	619304	619304	type	True	77.5001	114	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:01,666] [INFO] DFAST Taxonomy check result was written to GCF_001922575.1_ASM192257v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:01,667] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:01,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:01,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference/checkm_data
[2024-01-25 19:51:01,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:01,706] [INFO] Task started: CheckM
[2024-01-25 19:51:01,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001922575.1_ASM192257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001922575.1_ASM192257v1_genomic.fna/checkm_input GCF_001922575.1_ASM192257v1_genomic.fna/checkm_result
[2024-01-25 19:51:28,768] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:28,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:28,794] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:28,794] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:28,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001922575.1_ASM192257v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:28,795] [INFO] Task started: Blastn
[2024-01-25 19:51:28,795] [INFO] Running command: blastn -query GCF_001922575.1_ASM192257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55caa5ed-fb7d-4704-a7d0-9eae5e54436b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001922575.1_ASM192257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:29,622] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:29,625] [INFO] Selected 26 target genomes.
[2024-01-25 19:51:29,625] [INFO] Target genome list was writen to GCF_001922575.1_ASM192257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:29,663] [INFO] Task started: fastANI
[2024-01-25 19:51:29,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg2da37e8e-9b3f-41c5-8bd9-a1381587ce39/GCF_001922575.1_ASM192257v1_genomic.fna.gz --refList GCF_001922575.1_ASM192257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001922575.1_ASM192257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:45,760] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:45,768] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:45,768] [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_001922575.1	s__Neptunomonas phycophila	100.0	1282	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	98.55	98.14	0.96	0.94	4	conclusive
GCF_008630635.1	s__Neptunomonas concharum	78.9752	137	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCF_016592555.1	s__Neptunomonas japonica_A	78.6235	131	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001597725.1	s__Neptuniibacter marinus	77.8975	89	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422765.1	s__Neptunomonas japonica	77.7411	134	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153345.1	s__Neptuniibacter caesariensis	77.7388	70	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744175.1	s__Neptunomonas sp016744175	77.5993	125	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113275.1	s__Neptunomonas qingdaonensis	77.5674	125	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001305295.1	s__Neptunomonas antarctica	77.5113	116	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015209595.1	s__Pontibacterium sp015209595	77.2606	83	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435145.1	s__Neptuniibacter sp002435145	76.9893	62	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	99.91	99.87	0.93	0.93	3	-
GCA_016744155.1	s__Amphritea sp016744155	76.9334	61	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:45,769] [INFO] GTDB search result was written to GCF_001922575.1_ASM192257v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:45,770] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:45,772] [INFO] DFAST_QC result json was written to GCF_001922575.1_ASM192257v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:45,772] [INFO] DFAST_QC completed!
[2024-01-25 19:51:45,772] [INFO] Total running time: 0h1m10s