[2024-01-25 19:01:35,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:35,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:35,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference
[2024-01-25 19:01:36,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:36,842] [INFO] Task started: Prodigal
[2024-01-25 19:01:36,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgffba0f26-4485-4860-989c-7923061f62fc/GCF_003014655.1_ASM301465v1_genomic.fna.gz | prodigal -d GCF_003014655.1_ASM301465v1_genomic.fna/cds.fna -a GCF_003014655.1_ASM301465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:45,068] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:45,068] [INFO] Task started: HMMsearch
[2024-01-25 19:01:45,068] [INFO] Running command: hmmsearch --tblout GCF_003014655.1_ASM301465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference/reference_markers.hmm GCF_003014655.1_ASM301465v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:45,295] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:45,296] [INFO] Found 6/6 markers.
[2024-01-25 19:01:45,331] [INFO] Query marker FASTA was written to GCF_003014655.1_ASM301465v1_genomic.fna/markers.fasta
[2024-01-25 19:01:45,331] [INFO] Task started: Blastn
[2024-01-25 19:01:45,331] [INFO] Running command: blastn -query GCF_003014655.1_ASM301465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference/reference_markers.fasta -out GCF_003014655.1_ASM301465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:45,880] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:45,883] [INFO] Selected 22 target genomes.
[2024-01-25 19:01:45,883] [INFO] Target genome list was writen to GCF_003014655.1_ASM301465v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:45,911] [INFO] Task started: fastANI
[2024-01-25 19:01:45,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgffba0f26-4485-4860-989c-7923061f62fc/GCF_003014655.1_ASM301465v1_genomic.fna.gz --refList GCF_003014655.1_ASM301465v1_genomic.fna/target_genomes.txt --output GCF_003014655.1_ASM301465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:01:59,809] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:59,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:01:59,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:01:59,819] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:01:59,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:01:59,820] [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 glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	79.363	388	1180	95	below_threshold
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	79.3047	338	1180	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.0847	315	1180	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	79.0164	344	1180	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	79.0109	335	1180	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	78.9869	324	1180	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	78.9274	327	1180	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	78.8265	276	1180	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	78.7486	254	1180	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	78.7075	266	1180	95	below_threshold
Planococcus faecalis	strain=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	78.6819	244	1180	95	below_threshold
Planococcus salinus	strain=LCB217	GCA_003719725.1	1848460	1848460	type	True	78.4029	262	1180	95	below_threshold
Planococcus maritimus	strain=DSM 17275	GCA_001687625.2	192421	192421	type	True	78.2568	220	1180	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	77.0521	65	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:01:59,821] [INFO] DFAST Taxonomy check result was written to GCF_003014655.1_ASM301465v1_genomic.fna/tc_result.tsv
[2024-01-25 19:01:59,822] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:01:59,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:01:59,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference/checkm_data
[2024-01-25 19:01:59,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:01:59,860] [INFO] Task started: CheckM
[2024-01-25 19:01:59,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014655.1_ASM301465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014655.1_ASM301465v1_genomic.fna/checkm_input GCF_003014655.1_ASM301465v1_genomic.fna/checkm_result
[2024-01-25 19:02:27,884] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:27,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:27,904] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:27,904] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:27,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014655.1_ASM301465v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:27,906] [INFO] Task started: Blastn
[2024-01-25 19:02:27,906] [INFO] Running command: blastn -query GCF_003014655.1_ASM301465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38082191-5940-4ca2-a359-19daccbebf80/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014655.1_ASM301465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:28,675] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:28,678] [INFO] Selected 15 target genomes.
[2024-01-25 19:02:28,679] [INFO] Target genome list was writen to GCF_003014655.1_ASM301465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:28,715] [INFO] Task started: fastANI
[2024-01-25 19:02:28,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgffba0f26-4485-4860-989c-7923061f62fc/GCF_003014655.1_ASM301465v1_genomic.fna.gz --refList GCF_003014655.1_ASM301465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014655.1_ASM301465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:02:40,168] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:40,177] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:02:40,177] [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_003014655.1	s__Planococcus soli_A	100.0	1177	1180	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859275.1	s__Planococcus sp007859275	82.9879	845	1180	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	82.6595	797	1180	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_900099655.1	s__Planococcus glaciei	79.3535	388	1180	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_000821325.1	s__Planococcus massiliensis	79.3025	337	1180	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_004761975.1	s__Planococcus koreensis	79.0665	315	1180	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_016908095.1	s__Planococcus chinensis	79.0121	342	1180	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_018613575.1	s__Planococcus sp018613575	78.9374	310	1180	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	78.9354	326	1180	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_001687565.2	s__Planococcus antarcticus	78.8494	275	1180	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_007859295.1	s__Planococcus sp007859295	78.8103	338	1180	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_003668635.1	s__Planococcus sp003668635	78.8012	296	1180	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_001687625.2	s__Planococcus maritimus	78.2656	220	1180	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:02:40,179] [INFO] GTDB search result was written to GCF_003014655.1_ASM301465v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:02:40,179] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:02:40,182] [INFO] DFAST_QC result json was written to GCF_003014655.1_ASM301465v1_genomic.fna/dqc_result.json
[2024-01-25 19:02:40,182] [INFO] DFAST_QC completed!
[2024-01-25 19:02:40,182] [INFO] Total running time: 0h1m5s