[2024-01-24 11:19:55,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:55,193] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:55,193] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference
[2024-01-24 11:19:56,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:56,522] [INFO] Task started: Prodigal
[2024-01-24 11:19:56,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a52e35a-42be-42d4-97d6-0ca632df8bfe/GCF_017813365.1_ASM1781336v1_genomic.fna.gz | prodigal -d GCF_017813365.1_ASM1781336v1_genomic.fna/cds.fna -a GCF_017813365.1_ASM1781336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:12,756] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:12,757] [INFO] Task started: HMMsearch
[2024-01-24 11:20:12,757] [INFO] Running command: hmmsearch --tblout GCF_017813365.1_ASM1781336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference/reference_markers.hmm GCF_017813365.1_ASM1781336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:13,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:13,085] [INFO] Found 6/6 markers.
[2024-01-24 11:20:13,142] [INFO] Query marker FASTA was written to GCF_017813365.1_ASM1781336v1_genomic.fna/markers.fasta
[2024-01-24 11:20:13,143] [INFO] Task started: Blastn
[2024-01-24 11:20:13,143] [INFO] Running command: blastn -query GCF_017813365.1_ASM1781336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference/reference_markers.fasta -out GCF_017813365.1_ASM1781336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:14,064] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:14,068] [INFO] Selected 15 target genomes.
[2024-01-24 11:20:14,068] [INFO] Target genome list was writen to GCF_017813365.1_ASM1781336v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:14,075] [INFO] Task started: fastANI
[2024-01-24 11:20:14,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a52e35a-42be-42d4-97d6-0ca632df8bfe/GCF_017813365.1_ASM1781336v1_genomic.fna.gz --refList GCF_017813365.1_ASM1781336v1_genomic.fna/target_genomes.txt --output GCF_017813365.1_ASM1781336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:31,884] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:31,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:31,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:31,920] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:31,920] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:31,920] [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
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	83.6916	1038	1903	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	83.4037	1125	1903	95	below_threshold
Roseomonas aerilata	strain=DSM 19363	GCA_000711725.1	452982	452982	type	True	82.3477	1113	1903	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	82.2216	988	1903	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.2462	701	1903	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.9563	647	1903	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.9052	610	1903	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	78.5844	651	1903	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.3285	583	1903	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	78.1748	688	1903	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.1323	546	1903	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.0881	495	1903	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	77.889	673	1903	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	77.8781	610	1903	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	76.8649	343	1903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:31,922] [INFO] DFAST Taxonomy check result was written to GCF_017813365.1_ASM1781336v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:31,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:31,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:31,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference/checkm_data
[2024-01-24 11:20:31,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:31,985] [INFO] Task started: CheckM
[2024-01-24 11:20:31,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017813365.1_ASM1781336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017813365.1_ASM1781336v1_genomic.fna/checkm_input GCF_017813365.1_ASM1781336v1_genomic.fna/checkm_result
[2024-01-24 11:21:22,051] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:22,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:22,077] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:22,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:22,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017813365.1_ASM1781336v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:22,078] [INFO] Task started: Blastn
[2024-01-24 11:21:22,078] [INFO] Running command: blastn -query GCF_017813365.1_ASM1781336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c2df75-4b8a-4412-9b0b-304cffa0a9e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017813365.1_ASM1781336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:23,830] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:23,835] [INFO] Selected 7 target genomes.
[2024-01-24 11:21:23,835] [INFO] Target genome list was writen to GCF_017813365.1_ASM1781336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:23,864] [INFO] Task started: fastANI
[2024-01-24 11:21:23,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a52e35a-42be-42d4-97d6-0ca632df8bfe/GCF_017813365.1_ASM1781336v1_genomic.fna.gz --refList GCF_017813365.1_ASM1781336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017813365.1_ASM1781336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:34,230] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:34,245] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:34,245] [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_017813365.1	s__Roseomonas sp017813365	100.0	1901	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199205.1	s__Roseomonas pecuniae	83.6861	1039	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141905.1	s__Roseomonas rosea	83.394	1127	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813395.1	s__Roseomonas sp017813395	82.5987	1041	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	82.3528	1111	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848505.1	s__Roseomonas deserti_A	82.2344	985	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107305.1	s__Roseomonas sp016107305	82.1956	1062	1903	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:34,247] [INFO] GTDB search result was written to GCF_017813365.1_ASM1781336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:34,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:34,254] [INFO] DFAST_QC result json was written to GCF_017813365.1_ASM1781336v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:34,254] [INFO] DFAST_QC completed!
[2024-01-24 11:21:34,254] [INFO] Total running time: 0h1m39s