[2024-01-24 14:38:45,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference
[2024-01-24 14:38:48,275] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,277] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,278] [INFO] Running command: gunzip -c /var/lib/cwl/stg454c5346-94ef-4146-a97f-f504f142521f/GCF_008477545.1_ASM847754v1_genomic.fna.gz | prodigal -d GCF_008477545.1_ASM847754v1_genomic.fna/cds.fna -a GCF_008477545.1_ASM847754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:01,089] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:01,089] [INFO] Task started: HMMsearch
[2024-01-24 14:39:01,089] [INFO] Running command: hmmsearch --tblout GCF_008477545.1_ASM847754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference/reference_markers.hmm GCF_008477545.1_ASM847754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:01,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:01,408] [INFO] Found 6/6 markers.
[2024-01-24 14:39:01,450] [INFO] Query marker FASTA was written to GCF_008477545.1_ASM847754v1_genomic.fna/markers.fasta
[2024-01-24 14:39:01,450] [INFO] Task started: Blastn
[2024-01-24 14:39:01,451] [INFO] Running command: blastn -query GCF_008477545.1_ASM847754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference/reference_markers.fasta -out GCF_008477545.1_ASM847754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:02,591] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:02,595] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:02,595] [INFO] Target genome list was writen to GCF_008477545.1_ASM847754v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:02,621] [INFO] Task started: fastANI
[2024-01-24 14:39:02,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg454c5346-94ef-4146-a97f-f504f142521f/GCF_008477545.1_ASM847754v1_genomic.fna.gz --refList GCF_008477545.1_ASM847754v1_genomic.fna/target_genomes.txt --output GCF_008477545.1_ASM847754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:17,191] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:17,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:17,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:17,206] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:17,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:17,207] [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
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	100.0	1439	1439	95	conclusive
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	79.8315	598	1439	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	79.8191	653	1439	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	79.6425	584	1439	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	79.6424	576	1439	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	79.6338	585	1439	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	79.5994	691	1439	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	79.4777	552	1439	95	below_threshold
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	79.2265	543	1439	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	78.7158	472	1439	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	78.7134	475	1439	95	below_threshold
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	78.5657	483	1439	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.4625	440	1439	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.3577	325	1439	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.2699	234	1439	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.9906	260	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:17,209] [INFO] DFAST Taxonomy check result was written to GCF_008477545.1_ASM847754v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:17,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:17,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:17,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference/checkm_data
[2024-01-24 14:39:17,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:17,256] [INFO] Task started: CheckM
[2024-01-24 14:39:17,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008477545.1_ASM847754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008477545.1_ASM847754v1_genomic.fna/checkm_input GCF_008477545.1_ASM847754v1_genomic.fna/checkm_result
[2024-01-24 14:40:03,814] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:03,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:03,836] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:03,837] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:03,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008477545.1_ASM847754v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:03,837] [INFO] Task started: Blastn
[2024-01-24 14:40:03,838] [INFO] Running command: blastn -query GCF_008477545.1_ASM847754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56677aa1-ef90-4b85-969c-7265778cf63f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008477545.1_ASM847754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:06,106] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:06,110] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:06,110] [INFO] Target genome list was writen to GCF_008477545.1_ASM847754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:06,120] [INFO] Task started: fastANI
[2024-01-24 14:40:06,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg454c5346-94ef-4146-a97f-f504f142521f/GCF_008477545.1_ASM847754v1_genomic.fna.gz --refList GCF_008477545.1_ASM847754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008477545.1_ASM847754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:20,388] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:20,405] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:20,405] [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_008477545.1	s__Roseibium aestuarii	100.0	1439	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014842915.1	s__Roseibium litorale	79.8451	596	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142725.1	s__Roseibium suaedae	79.8273	652	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009915765.1	s__Pannonibacter sp009915765	79.7003	604	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_001418225.1	s__Pannonibacter indicus	79.6514	583	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_017313085.1	s__Roseibium sp017313085	79.5955	692	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	79.5625	651	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	79.5592	584	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	79.2256	544	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237595.1	s__Roseibium sp002237595	79.1159	526	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075075.1	s__Roseibium sp003075075	79.0583	544	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	78.8952	534	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_001696535.1	s__Stappia indica	78.7666	561	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_900185725.1	s__Stappia sp900185725	78.662	536	1439	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:20,407] [INFO] GTDB search result was written to GCF_008477545.1_ASM847754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:20,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:20,415] [INFO] DFAST_QC result json was written to GCF_008477545.1_ASM847754v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:20,416] [INFO] DFAST_QC completed!
[2024-01-24 14:40:20,416] [INFO] Total running time: 0h1m35s