[2024-01-24 13:57:42,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,905] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,905] [INFO] DQC Reference Directory: /var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference
[2024-01-24 13:57:44,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,145] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg21006f28-6f1e-400a-b896-20cc64bde629/GCF_006148955.1_ASM614895v1_genomic.fna.gz | prodigal -d GCF_006148955.1_ASM614895v1_genomic.fna/cds.fna -a GCF_006148955.1_ASM614895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:52,685] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:52,686] [INFO] Task started: HMMsearch
[2024-01-24 13:57:52,686] [INFO] Running command: hmmsearch --tblout GCF_006148955.1_ASM614895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference/reference_markers.hmm GCF_006148955.1_ASM614895v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:53,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:53,050] [INFO] Found 6/6 markers.
[2024-01-24 13:57:53,084] [INFO] Query marker FASTA was written to GCF_006148955.1_ASM614895v1_genomic.fna/markers.fasta
[2024-01-24 13:57:53,085] [INFO] Task started: Blastn
[2024-01-24 13:57:53,085] [INFO] Running command: blastn -query GCF_006148955.1_ASM614895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference/reference_markers.fasta -out GCF_006148955.1_ASM614895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:53,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:53,743] [INFO] Selected 26 target genomes.
[2024-01-24 13:57:53,743] [INFO] Target genome list was writen to GCF_006148955.1_ASM614895v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:53,754] [INFO] Task started: fastANI
[2024-01-24 13:57:53,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg21006f28-6f1e-400a-b896-20cc64bde629/GCF_006148955.1_ASM614895v1_genomic.fna.gz --refList GCF_006148955.1_ASM614895v1_genomic.fna/target_genomes.txt --output GCF_006148955.1_ASM614895v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:10,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:10,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:10,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:10,344] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:10,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:10,345] [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 concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	100.0	1185	1205	95	conclusive
Neptunomonas concharum	strain=JCM17730	GCA_008630635.1	1031538	1031538	type	True	99.999	1168	1205	95	conclusive
Neptunomonas phycophila	strain=CECT 8716	GCA_001922575.1	1572645	1572645	type	True	78.6936	127	1205	95	below_threshold
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	78.5735	158	1205	95	below_threshold
Neptunomonas japonica	strain=DSM 18939	GCA_000422765.1	417574	417574	type	True	77.846	215	1205	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	77.7163	221	1205	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	77.6726	216	1205	95	below_threshold
Nitrincola tapanii	strain=MEB193	GCA_008368715.1	1708751	1708751	type	True	77.4445	67	1205	95	below_threshold
Neptuniibacter pectenicola	strain=LFT 1.8	GCA_001597735.1	1806669	1806669	type	True	77.3997	92	1205	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	77.3768	80	1205	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	77.3538	91	1205	95	below_threshold
Nitrincola alkalilacustris	strain=NCAIM B.02612	GCA_008973755.1	1571224	1571224	type	True	77.2298	57	1205	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	77.1859	102	1205	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	77.0538	64	1205	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	77.0353	77	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:10,346] [INFO] DFAST Taxonomy check result was written to GCF_006148955.1_ASM614895v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:10,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:10,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:10,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference/checkm_data
[2024-01-24 13:58:10,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:10,385] [INFO] Task started: CheckM
[2024-01-24 13:58:10,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006148955.1_ASM614895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006148955.1_ASM614895v1_genomic.fna/checkm_input GCF_006148955.1_ASM614895v1_genomic.fna/checkm_result
[2024-01-24 13:58:42,065] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:42,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:42,092] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:42,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:42,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006148955.1_ASM614895v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:42,094] [INFO] Task started: Blastn
[2024-01-24 13:58:42,095] [INFO] Running command: blastn -query GCF_006148955.1_ASM614895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg639d0d18-6a4e-4f57-96ae-776fddac5db2/dqc_reference/reference_markers_gtdb.fasta -out GCF_006148955.1_ASM614895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:42,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:42,993] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:42,993] [INFO] Target genome list was writen to GCF_006148955.1_ASM614895v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:43,104] [INFO] Task started: fastANI
[2024-01-24 13:58:43,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg21006f28-6f1e-400a-b896-20cc64bde629/GCF_006148955.1_ASM614895v1_genomic.fna.gz --refList GCF_006148955.1_ASM614895v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006148955.1_ASM614895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:57,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:57,783] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:57,783] [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_008630635.1	s__Neptunomonas concharum	99.999	1168	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCF_001922575.1	s__Neptunomonas phycophila	78.6608	126	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	98.55	98.14	0.96	0.94	4	-
GCF_004005935.1	s__Neptunomonas marina	78.5735	158	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	97.03	97.03	0.93	0.93	2	-
GCF_016592555.1	s__Neptunomonas japonica_A	78.2478	217	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744175.1	s__Neptunomonas sp016744175	77.8872	175	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422765.1	s__Neptunomonas japonica	77.8669	210	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860855.1	s__Amphritea atlantica_A	77.7238	78	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113275.1	s__Neptunomonas qingdaonensis	77.7204	220	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008368715.1	s__Nitrincola tapanii	77.6288	62	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111095.1	s__Amphritea atlantica	77.3925	79	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001597735.1	s__Neptuniibacter pectenicola	77.3711	92	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
GCF_003858655.1	s__Amphritea balenae	77.3131	87	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003957515.1	s__Amphritea opalescens	77.3025	92	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153345.1	s__Neptuniibacter caesariensis	77.1724	101	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973755.1	s__Nitrincola alkalilacustris	77.1664	56	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	77.1178	75	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	76.9823	64	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	76.8301	58	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:57,792] [INFO] GTDB search result was written to GCF_006148955.1_ASM614895v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:57,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:57,799] [INFO] DFAST_QC result json was written to GCF_006148955.1_ASM614895v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:57,799] [INFO] DFAST_QC completed!
[2024-01-24 13:58:57,799] [INFO] Total running time: 0h1m15s