[2024-01-24 10:47:11,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,668] [INFO] DQC Reference Directory: /var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1129c40-c739-42f1-bd8a-4d68e944a086/GCF_003990445.1_ASM399044v1_genomic.fna.gz | prodigal -d GCF_003990445.1_ASM399044v1_genomic.fna/cds.fna -a GCF_003990445.1_ASM399044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:33,973] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:33,974] [INFO] Task started: HMMsearch
[2024-01-24 10:47:33,974] [INFO] Running command: hmmsearch --tblout GCF_003990445.1_ASM399044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference/reference_markers.hmm GCF_003990445.1_ASM399044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:34,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:34,261] [INFO] Found 6/6 markers.
[2024-01-24 10:47:34,304] [INFO] Query marker FASTA was written to GCF_003990445.1_ASM399044v1_genomic.fna/markers.fasta
[2024-01-24 10:47:34,304] [INFO] Task started: Blastn
[2024-01-24 10:47:34,304] [INFO] Running command: blastn -query GCF_003990445.1_ASM399044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference/reference_markers.fasta -out GCF_003990445.1_ASM399044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:35,268] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:35,272] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:35,272] [INFO] Target genome list was writen to GCF_003990445.1_ASM399044v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:35,278] [INFO] Task started: fastANI
[2024-01-24 10:47:35,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1129c40-c739-42f1-bd8a-4d68e944a086/GCF_003990445.1_ASM399044v1_genomic.fna.gz --refList GCF_003990445.1_ASM399044v1_genomic.fna/target_genomes.txt --output GCF_003990445.1_ASM399044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:48,936] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:48,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:48,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:48,952] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:48,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:48,952] [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
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	100.0	1589	1591	95	conclusive
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	81.6138	991	1591	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	81.6084	999	1591	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	81.2764	907	1591	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	79.0031	678	1591	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.0365	473	1591	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.9758	361	1591	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.911	410	1591	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8476	390	1591	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.8328	407	1591	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.8109	319	1591	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.7894	394	1591	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.6623	366	1591	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	77.6159	395	1591	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	77.5573	355	1591	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.4954	401	1591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:48,954] [INFO] DFAST Taxonomy check result was written to GCF_003990445.1_ASM399044v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:48,955] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:48,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:48,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference/checkm_data
[2024-01-24 10:47:48,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:49,004] [INFO] Task started: CheckM
[2024-01-24 10:47:49,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990445.1_ASM399044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990445.1_ASM399044v1_genomic.fna/checkm_input GCF_003990445.1_ASM399044v1_genomic.fna/checkm_result
[2024-01-24 10:48:36,611] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:36,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:36,639] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:36,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:36,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990445.1_ASM399044v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:36,640] [INFO] Task started: Blastn
[2024-01-24 10:48:36,640] [INFO] Running command: blastn -query GCF_003990445.1_ASM399044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf676a150-7ea0-41de-b258-0a44635aff00/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990445.1_ASM399044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:38,388] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:38,393] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:38,393] [INFO] Target genome list was writen to GCF_003990445.1_ASM399044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:38,423] [INFO] Task started: fastANI
[2024-01-24 10:48:38,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1129c40-c739-42f1-bd8a-4d68e944a086/GCF_003990445.1_ASM399044v1_genomic.fna.gz --refList GCF_003990445.1_ASM399044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990445.1_ASM399044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:48,131] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,157] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:48,158] [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_003990445.1	s__Pararhodobacter zhoushanensis	100.0	1589	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017303295.1	s__Pararhodobacter sp017303295	81.8323	933	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	81.6174	997	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003122215.1	s__Pararhodobacter marinus	81.281	906	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691415.1	s__Pararhodobacter sp001691415	81.1395	933	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479725.1	s__Pararhodobacter sp905479725	79.0388	361	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.4807	528	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551925.1	s__PUOA01 sp003551925	77.8109	341	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011174775.1	s__Tabrizicola sp011174775	77.4957	401	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792685.1	s__Tabrizicola sp016792685	77.1105	283	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	77.0988	234	1591	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,160] [INFO] GTDB search result was written to GCF_003990445.1_ASM399044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:48,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:48,164] [INFO] DFAST_QC result json was written to GCF_003990445.1_ASM399044v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:48,165] [INFO] DFAST_QC completed!
[2024-01-24 10:48:48,165] [INFO] Total running time: 0h1m36s