[2024-01-24 11:48:21,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,565] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,566] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3842084-d44a-43d5-ac17-34ede57d071e/GCF_022819085.1_ASM2281908v1_genomic.fna.gz | prodigal -d GCF_022819085.1_ASM2281908v1_genomic.fna/cds.fna -a GCF_022819085.1_ASM2281908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:33,864] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:33,865] [INFO] Task started: HMMsearch
[2024-01-24 11:48:33,865] [INFO] Running command: hmmsearch --tblout GCF_022819085.1_ASM2281908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference/reference_markers.hmm GCF_022819085.1_ASM2281908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:34,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:34,121] [INFO] Found 6/6 markers.
[2024-01-24 11:48:34,153] [INFO] Query marker FASTA was written to GCF_022819085.1_ASM2281908v1_genomic.fna/markers.fasta
[2024-01-24 11:48:34,153] [INFO] Task started: Blastn
[2024-01-24 11:48:34,153] [INFO] Running command: blastn -query GCF_022819085.1_ASM2281908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference/reference_markers.fasta -out GCF_022819085.1_ASM2281908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:34,769] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:34,773] [INFO] Selected 15 target genomes.
[2024-01-24 11:48:34,774] [INFO] Target genome list was writen to GCF_022819085.1_ASM2281908v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:34,843] [INFO] Task started: fastANI
[2024-01-24 11:48:34,843] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3842084-d44a-43d5-ac17-34ede57d071e/GCF_022819085.1_ASM2281908v1_genomic.fna.gz --refList GCF_022819085.1_ASM2281908v1_genomic.fna/target_genomes.txt --output GCF_022819085.1_ASM2281908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:45,340] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:45,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:45,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:45,355] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:48:45,355] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:48:45,355] [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
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	100.0	1118	1118	95	inconclusive
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	97.8636	1042	1118	95	inconclusive
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	80.1588	529	1118	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.5875	419	1118	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.5368	422	1118	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	79.1571	396	1118	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	78.8803	314	1118	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	78.7738	307	1118	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	78.7052	373	1118	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	78.4418	307	1118	95	below_threshold
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	78.3629	327	1118	95	below_threshold
Planococcus maritimus	strain=DSM 17275	GCA_001687625.2	192421	192421	type	True	78.3443	274	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:45,357] [INFO] DFAST Taxonomy check result was written to GCF_022819085.1_ASM2281908v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:45,357] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:45,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:45,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference/checkm_data
[2024-01-24 11:48:45,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:45,392] [INFO] Task started: CheckM
[2024-01-24 11:48:45,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022819085.1_ASM2281908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022819085.1_ASM2281908v1_genomic.fna/checkm_input GCF_022819085.1_ASM2281908v1_genomic.fna/checkm_result
[2024-01-24 11:49:17,349] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:17,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:17,368] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:17,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:17,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022819085.1_ASM2281908v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:17,370] [INFO] Task started: Blastn
[2024-01-24 11:49:17,370] [INFO] Running command: blastn -query GCF_022819085.1_ASM2281908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5fb3267-45b3-47d4-9fd8-b373af12a801/dqc_reference/reference_markers_gtdb.fasta -out GCF_022819085.1_ASM2281908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:18,166] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:18,169] [INFO] Selected 18 target genomes.
[2024-01-24 11:49:18,169] [INFO] Target genome list was writen to GCF_022819085.1_ASM2281908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:18,182] [INFO] Task started: fastANI
[2024-01-24 11:49:18,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3842084-d44a-43d5-ac17-34ede57d071e/GCF_022819085.1_ASM2281908v1_genomic.fna.gz --refList GCF_022819085.1_ASM2281908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022819085.1_ASM2281908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:49:29,934] [INFO] Task succeeded: fastANI
[2024-01-24 11:49:29,950] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:49:29,950] [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_000821325.1	s__Planococcus massiliensis	97.8636	1042	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900099655.1	s__Planococcus glaciei	80.1481	530	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.05	96.92	0.90	0.89	5	-
GCF_016908095.1	s__Planococcus chinensis	79.6968	454	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761975.1	s__Planococcus koreensis	79.5246	423	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007859295.1	s__Planococcus sp007859295	79.3096	351	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428875.1	s__Planococcus okeanokoites	79.294	333	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.50	97.25	0.88	0.87	3	-
GCF_007859275.1	s__Planococcus sp007859275	79.28	381	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859395.1	s__Planococcus sp007859395	79.2019	374	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014655.1	s__Planococcus soli_A	79.1608	340	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836985.1	s__Planococcus sp014836985	79.1571	396	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.16	97.16	0.91	0.91	2	-
GCF_017873465.1	s__Planococcus mcmeekinii	79.0536	354	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785555.1	s__Planococcus sp000785555	79.0252	268	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820495.1	s__Planococcus sp016820495	78.9763	332	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687565.2	s__Planococcus antarcticus	78.8891	314	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.42	99.42	0.95	0.95	2	-
GCF_016881065.1	s__Planococcus soli	78.7052	373	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007004625.1	s__Planococcus salinarum	78.5589	330	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018283455.1	s__Planococcus sp018283455	78.546	325	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613655.1	s__Planococcus sp018613655	78.1634	283	1118	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:49:29,952] [INFO] GTDB search result was written to GCF_022819085.1_ASM2281908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:49:29,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:49:29,957] [INFO] DFAST_QC result json was written to GCF_022819085.1_ASM2281908v1_genomic.fna/dqc_result.json
[2024-01-24 11:49:29,958] [INFO] DFAST_QC completed!
[2024-01-24 11:49:29,958] [INFO] Total running time: 0h1m9s