[2024-01-24 13:40:34,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference
[2024-01-24 13:40:35,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,783] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg71553b4a-5af4-4545-885f-c3fd1aac38f3/GCF_001661965.1_ASM166196v1_genomic.fna.gz | prodigal -d GCF_001661965.1_ASM166196v1_genomic.fna/cds.fna -a GCF_001661965.1_ASM166196v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,839] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,839] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,839] [INFO] Running command: hmmsearch --tblout GCF_001661965.1_ASM166196v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference/reference_markers.hmm GCF_001661965.1_ASM166196v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,182] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,222] [INFO] Query marker FASTA was written to GCF_001661965.1_ASM166196v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,223] [INFO] Task started: Blastn
[2024-01-24 13:40:49,223] [INFO] Running command: blastn -query GCF_001661965.1_ASM166196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference/reference_markers.fasta -out GCF_001661965.1_ASM166196v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,225] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,228] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:50,229] [INFO] Target genome list was writen to GCF_001661965.1_ASM166196v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,235] [INFO] Task started: fastANI
[2024-01-24 13:40:50,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg71553b4a-5af4-4545-885f-c3fd1aac38f3/GCF_001661965.1_ASM166196v1_genomic.fna.gz --refList GCF_001661965.1_ASM166196v1_genomic.fna/target_genomes.txt --output GCF_001661965.1_ASM166196v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:02,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:02,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:02,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:02,123] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:02,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:02,123] [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
Croceicoccus mobilis	strain=Ery22	GCA_001661965.1	1703339	1703339	type	True	100.0	1383	1389	95	conclusive
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	99.9821	1356	1389	95	conclusive
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	82.6649	735	1389	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	81.1545	555	1389	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	80.198	520	1389	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	79.9155	512	1389	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	79.2686	461	1389	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000767465.1	205844	205844	type	True	79.1677	374	1389	95	below_threshold
Novosphingobium pentaromativorans	strain=US6-1	GCA_000235975.2	205844	205844	type	True	78.9782	362	1389	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.9118	352	1389	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.762	324	1389	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.6563	361	1389	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.4568	328	1389	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.3939	345	1389	95	below_threshold
Aurantiacibacter gangjinensis	strain=K7-2	GCA_001010925.1	502682	502682	type	True	77.989	268	1389	95	below_threshold
Aurantiacibacter gangjinensis	strain=CGMCC 1.15024	GCA_001886695.1	502682	502682	type	True	77.9866	269	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:02,125] [INFO] DFAST Taxonomy check result was written to GCF_001661965.1_ASM166196v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:02,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:02,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:02,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference/checkm_data
[2024-01-24 13:41:02,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:02,171] [INFO] Task started: CheckM
[2024-01-24 13:41:02,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001661965.1_ASM166196v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001661965.1_ASM166196v1_genomic.fna/checkm_input GCF_001661965.1_ASM166196v1_genomic.fna/checkm_result
[2024-01-24 13:41:44,620] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:44,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,642] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:44,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:44,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001661965.1_ASM166196v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:44,644] [INFO] Task started: Blastn
[2024-01-24 13:41:44,644] [INFO] Running command: blastn -query GCF_001661965.1_ASM166196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa5b37b-d8c7-4c29-a398-7d9c3491c622/dqc_reference/reference_markers_gtdb.fasta -out GCF_001661965.1_ASM166196v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,596] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,601] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:46,601] [INFO] Target genome list was writen to GCF_001661965.1_ASM166196v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,612] [INFO] Task started: fastANI
[2024-01-24 13:41:46,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg71553b4a-5af4-4545-885f-c3fd1aac38f3/GCF_001661965.1_ASM166196v1_genomic.fna.gz --refList GCF_001661965.1_ASM166196v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001661965.1_ASM166196v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:57,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:57,870] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:57,870] [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_001661965.1	s__Croceicoccus mobilis	100.0	1382	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001661675.2	s__Croceicoccus marinus	82.6438	735	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	-
GCA_002694745.1	s__Croceicoccus sp002694745	82.5514	670	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	99.91	99.91	0.91	0.91	2	-
GCF_018398395.1	s__Croceicoccus sp018398395	81.1427	556	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661915.1	s__Croceicoccus pelagius	80.2132	519	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007570835.1	s__Croceicoccus sediminis	79.9052	513	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745095.1	s__Croceicoccus sp016745095	79.5464	465	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767465.1	s__Novosphingobium pentaromativorans	79.1888	373	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	96.84	95.17	0.76	0.62	4	-
GCF_003454795.1	s__Novosphingobium sp003454795	78.9639	350	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.02	97.88	0.92	0.91	3	-
GCF_007993975.1	s__Novosphingobium barchaimii_B	78.3689	369	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745295.1	s__Novosphingobium sp017745295	78.2145	338	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660445.1	s__Croceibacterium ferulae	78.2058	322	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886695.1	s__Alteraurantiacibacter gangjinensis	77.9965	269	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903970225.1	s__Novosphingobium sp903970225	77.4083	227	1389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:57,872] [INFO] GTDB search result was written to GCF_001661965.1_ASM166196v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:57,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:57,877] [INFO] DFAST_QC result json was written to GCF_001661965.1_ASM166196v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:57,877] [INFO] DFAST_QC completed!
[2024-01-24 13:41:57,877] [INFO] Total running time: 0h1m23s