[2024-01-25 18:15:05,586] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:05,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:05,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference
[2024-01-25 18:15:06,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:06,708] [INFO] Task started: Prodigal
[2024-01-25 18:15:06,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg6461b222-8a38-4204-9a96-3aa2d8df13d7/GCF_014635285.1_ASM1463528v1_genomic.fna.gz | prodigal -d GCF_014635285.1_ASM1463528v1_genomic.fna/cds.fna -a GCF_014635285.1_ASM1463528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:19,155] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:19,155] [INFO] Task started: HMMsearch
[2024-01-25 18:15:19,155] [INFO] Running command: hmmsearch --tblout GCF_014635285.1_ASM1463528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference/reference_markers.hmm GCF_014635285.1_ASM1463528v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:19,394] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:19,394] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6461b222-8a38-4204-9a96-3aa2d8df13d7/GCF_014635285.1_ASM1463528v1_genomic.fna.gz]
[2024-01-25 18:15:19,431] [INFO] Query marker FASTA was written to GCF_014635285.1_ASM1463528v1_genomic.fna/markers.fasta
[2024-01-25 18:15:19,432] [INFO] Task started: Blastn
[2024-01-25 18:15:19,432] [INFO] Running command: blastn -query GCF_014635285.1_ASM1463528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference/reference_markers.fasta -out GCF_014635285.1_ASM1463528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:20,243] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:20,248] [INFO] Selected 16 target genomes.
[2024-01-25 18:15:20,249] [INFO] Target genome list was writen to GCF_014635285.1_ASM1463528v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:20,269] [INFO] Task started: fastANI
[2024-01-25 18:15:20,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg6461b222-8a38-4204-9a96-3aa2d8df13d7/GCF_014635285.1_ASM1463528v1_genomic.fna.gz --refList GCF_014635285.1_ASM1463528v1_genomic.fna/target_genomes.txt --output GCF_014635285.1_ASM1463528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:35,430] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:35,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:35,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:35,441] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:15:35,441] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:35,441] [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
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	100.0	1463	1465	95	conclusive
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	99.9971	1448	1465	95	conclusive
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	80.6169	805	1465	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.9431	551	1465	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	78.6155	480	1465	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	78.5705	478	1465	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	78.5534	483	1465	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	78.5362	485	1465	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	77.7061	355	1465	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.1758	318	1465	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	77.055	282	1465	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.9509	297	1465	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.9234	296	1465	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9062	293	1465	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.7941	229	1465	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.3109	285	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:35,442] [INFO] DFAST Taxonomy check result was written to GCF_014635285.1_ASM1463528v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:35,443] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:35,443] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:35,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference/checkm_data
[2024-01-25 18:15:35,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:35,484] [INFO] Task started: CheckM
[2024-01-25 18:15:35,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635285.1_ASM1463528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635285.1_ASM1463528v1_genomic.fna/checkm_input GCF_014635285.1_ASM1463528v1_genomic.fna/checkm_result
[2024-01-25 18:16:25,068] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:25,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:25,100] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:25,101] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:25,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635285.1_ASM1463528v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:25,102] [INFO] Task started: Blastn
[2024-01-25 18:16:25,102] [INFO] Running command: blastn -query GCF_014635285.1_ASM1463528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dd74aaf-987a-481e-a416-d4e7c3e6c1df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635285.1_ASM1463528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:26,568] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:26,571] [INFO] Selected 7 target genomes.
[2024-01-25 18:16:26,571] [INFO] Target genome list was writen to GCF_014635285.1_ASM1463528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:26,583] [INFO] Task started: fastANI
[2024-01-25 18:16:26,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg6461b222-8a38-4204-9a96-3aa2d8df13d7/GCF_014635285.1_ASM1463528v1_genomic.fna.gz --refList GCF_014635285.1_ASM1463528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635285.1_ASM1463528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:33,973] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:33,979] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:33,979] [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_014635285.1	s__Stappia taiwanensis	100.0	1463	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900185725.1	s__Stappia sp900185725	81.2624	820	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCA_002709505.1	s__Stappia sp002709505	80.9735	700	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789575.1	s__Stappia indica_A	80.96	869	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	80.8591	834	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_001696535.1	s__Stappia indica	80.7946	862	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_000423705.1	s__Stappia stellulata	80.6242	804	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:33,980] [INFO] GTDB search result was written to GCF_014635285.1_ASM1463528v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:33,980] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:33,983] [INFO] DFAST_QC result json was written to GCF_014635285.1_ASM1463528v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:33,983] [INFO] DFAST_QC completed!
[2024-01-25 18:16:33,983] [INFO] Total running time: 0h1m28s