[2024-01-24 14:47:19,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference
[2024-01-24 14:47:21,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,208] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,209] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0d8c0c4-b2a5-499d-9a8f-1bc85eb831f5/GCF_003574655.1_ASM357465v1_genomic.fna.gz | prodigal -d GCF_003574655.1_ASM357465v1_genomic.fna/cds.fna -a GCF_003574655.1_ASM357465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:36,942] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:36,943] [INFO] Task started: HMMsearch
[2024-01-24 14:47:36,943] [INFO] Running command: hmmsearch --tblout GCF_003574655.1_ASM357465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference/reference_markers.hmm GCF_003574655.1_ASM357465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:37,244] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:37,245] [INFO] Found 6/6 markers.
[2024-01-24 14:47:37,300] [INFO] Query marker FASTA was written to GCF_003574655.1_ASM357465v1_genomic.fna/markers.fasta
[2024-01-24 14:47:37,301] [INFO] Task started: Blastn
[2024-01-24 14:47:37,301] [INFO] Running command: blastn -query GCF_003574655.1_ASM357465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference/reference_markers.fasta -out GCF_003574655.1_ASM357465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:38,268] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:38,271] [INFO] Selected 18 target genomes.
[2024-01-24 14:47:38,271] [INFO] Target genome list was writen to GCF_003574655.1_ASM357465v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:38,352] [INFO] Task started: fastANI
[2024-01-24 14:47:38,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0d8c0c4-b2a5-499d-9a8f-1bc85eb831f5/GCF_003574655.1_ASM357465v1_genomic.fna.gz --refList GCF_003574655.1_ASM357465v1_genomic.fna/target_genomes.txt --output GCF_003574655.1_ASM357465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:55,822] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:55,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:55,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:55,839] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:55,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:55,839] [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
Cohaesibacter haloalkalitolerans	strain=JC131	GCA_003574655.1	1162980	1162980	type	True	100.0	1656	1658	95	conclusive
Cohaesibacter marisflavi	strain=CGMCC 1.9157	GCA_900115225.1	655353	655353	type	True	81.4041	1048	1658	95	below_threshold
Cohaesibacter intestini	strain=YE-B6	GCA_003324485.1	2211145	2211145	type	True	78.3762	491	1658	95	below_threshold
Cohaesibacter gelatinilyticus	strain=DSM 18289	GCA_900215605.1	372072	372072	type	True	77.7384	184	1658	95	below_threshold
Cohaesibacter celericrescens	strain=H1304	GCA_002866925.1	2067669	2067669	type	True	77.2103	261	1658	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.7677	119	1658	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	76.5898	169	1658	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	76.5219	146	1658	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.446	139	1658	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	76.4031	144	1658	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.3887	148	1658	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	76.246	123	1658	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	76.1716	105	1658	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.0698	134	1658	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	76.0489	140	1658	95	below_threshold
Phyllobacterium trifolii	strain=CECT 7015	GCA_014192095.1	300193	300193	type	True	76.0323	62	1658	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	76.0263	142	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:55,841] [INFO] DFAST Taxonomy check result was written to GCF_003574655.1_ASM357465v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:55,842] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:55,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:55,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference/checkm_data
[2024-01-24 14:47:55,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:55,898] [INFO] Task started: CheckM
[2024-01-24 14:47:55,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574655.1_ASM357465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574655.1_ASM357465v1_genomic.fna/checkm_input GCF_003574655.1_ASM357465v1_genomic.fna/checkm_result
[2024-01-24 14:48:46,852] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:46,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:46,873] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:46,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:46,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574655.1_ASM357465v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:46,874] [INFO] Task started: Blastn
[2024-01-24 14:48:46,874] [INFO] Running command: blastn -query GCF_003574655.1_ASM357465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3790ea44-cacf-4542-b540-d70d5a0b8e0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574655.1_ASM357465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:48,659] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:48,663] [INFO] Selected 12 target genomes.
[2024-01-24 14:48:48,663] [INFO] Target genome list was writen to GCF_003574655.1_ASM357465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:48,695] [INFO] Task started: fastANI
[2024-01-24 14:48:48,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0d8c0c4-b2a5-499d-9a8f-1bc85eb831f5/GCF_003574655.1_ASM357465v1_genomic.fna.gz --refList GCF_003574655.1_ASM357465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574655.1_ASM357465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:59,951] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:59,962] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:59,962] [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_003574655.1	s__Cohaesibacter haloalkalitolerans	100.0	1656	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115225.1	s__Cohaesibacter marisflavi	81.4041	1048	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215505.1	s__Cohaesibacter sp900215505	78.8938	501	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324485.1	s__Cohaesibacter intestini	78.3786	490	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	98.38	98.38	0.96	0.96	2	-
GCF_002866925.1	s__Cohaesibacter celericrescens	77.1894	263	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	76.5933	161	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	76.3055	123	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_000423705.1	s__Stappia stellulata	76.2171	125	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	76.1953	106	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_900105595.1	s__Stappia sp900105595	76.1357	126	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709505.1	s__Stappia sp002709505	76.0026	132	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	75.9693	120	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:59,964] [INFO] GTDB search result was written to GCF_003574655.1_ASM357465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:59,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:59,968] [INFO] DFAST_QC result json was written to GCF_003574655.1_ASM357465v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:59,968] [INFO] DFAST_QC completed!
[2024-01-24 14:48:59,969] [INFO] Total running time: 0h1m40s