[2024-01-24 13:17:33,728] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference
[2024-01-24 13:17:35,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,134] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,134] [INFO] Running command: gunzip -c /var/lib/cwl/stgc38437fd-4895-445a-ab33-09b28ebbd480/GCF_012272835.1_ASM1227283v1_genomic.fna.gz | prodigal -d GCF_012272835.1_ASM1227283v1_genomic.fna/cds.fna -a GCF_012272835.1_ASM1227283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:48,760] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:48,761] [INFO] Task started: HMMsearch
[2024-01-24 13:17:48,761] [INFO] Running command: hmmsearch --tblout GCF_012272835.1_ASM1227283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference/reference_markers.hmm GCF_012272835.1_ASM1227283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:49,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:49,142] [INFO] Found 6/6 markers.
[2024-01-24 13:17:49,183] [INFO] Query marker FASTA was written to GCF_012272835.1_ASM1227283v1_genomic.fna/markers.fasta
[2024-01-24 13:17:49,184] [INFO] Task started: Blastn
[2024-01-24 13:17:49,184] [INFO] Running command: blastn -query GCF_012272835.1_ASM1227283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference/reference_markers.fasta -out GCF_012272835.1_ASM1227283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:49,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:49,993] [INFO] Selected 21 target genomes.
[2024-01-24 13:17:49,993] [INFO] Target genome list was writen to GCF_012272835.1_ASM1227283v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:50,001] [INFO] Task started: fastANI
[2024-01-24 13:17:50,001] [INFO] Running command: fastANI --query /var/lib/cwl/stgc38437fd-4895-445a-ab33-09b28ebbd480/GCF_012272835.1_ASM1227283v1_genomic.fna.gz --refList GCF_012272835.1_ASM1227283v1_genomic.fna/target_genomes.txt --output GCF_012272835.1_ASM1227283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:05,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:05,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:05,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:05,495] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:05,496] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:05,496] [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
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	100.0	1460	1461	95	conclusive
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	78.8093	318	1461	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	78.0396	243	1461	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.999	239	1461	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.5729	196	1461	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	77.4149	186	1461	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	77.4065	187	1461	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	77.3256	65	1461	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	76.6909	53	1461	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	76.6514	54	1461	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	76.0674	52	1461	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.0479	61	1461	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	76.0315	68	1461	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.9322	69	1461	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	75.8775	52	1461	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:05,498] [INFO] DFAST Taxonomy check result was written to GCF_012272835.1_ASM1227283v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:05,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:05,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:05,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference/checkm_data
[2024-01-24 13:18:05,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:05,541] [INFO] Task started: CheckM
[2024-01-24 13:18:05,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012272835.1_ASM1227283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012272835.1_ASM1227283v1_genomic.fna/checkm_input GCF_012272835.1_ASM1227283v1_genomic.fna/checkm_result
[2024-01-24 13:18:47,397] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:47,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:47,418] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:47,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:47,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012272835.1_ASM1227283v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:47,420] [INFO] Task started: Blastn
[2024-01-24 13:18:47,420] [INFO] Running command: blastn -query GCF_012272835.1_ASM1227283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg825f5f53-b03d-4e5f-bf8c-b27201691d20/dqc_reference/reference_markers_gtdb.fasta -out GCF_012272835.1_ASM1227283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,801] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:48,802] [INFO] Target genome list was writen to GCF_012272835.1_ASM1227283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:48,824] [INFO] Task started: fastANI
[2024-01-24 13:18:48,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgc38437fd-4895-445a-ab33-09b28ebbd480/GCF_012272835.1_ASM1227283v1_genomic.fna.gz --refList GCF_012272835.1_ASM1227283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012272835.1_ASM1227283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:00,668] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:00,685] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:00,685] [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_012272835.1	s__Spongiibacter sp012272835	100.0	1460	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420325.1	s__Spongiibacter tropicus	78.8093	318	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_000422345.1	s__Spongiibacter marinus_A	78.3259	251	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906995.1	s__Spongiibacter marinus	78.2861	275	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_016132545.1	s__CSC3-9 sp016132545	78.0137	240	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	77.5538	198	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	77.4545	161	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010805.1	s__IMCC21906 sp001010805	77.3738	175	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710725.1	s__Litorivivens sp002710725	77.2228	129	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066965.1	s__Marortus sp018066965	76.9973	130	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.4903	102	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016132445.1	s__UBA2009 sp016132445	76.2787	55	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCF_900107725.1	s__Microbulbifer marinus	76.2493	79	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309075.1	s__Motiliproteus sp017309075	76.0131	54	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	75.7948	63	1461	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:00,687] [INFO] GTDB search result was written to GCF_012272835.1_ASM1227283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:00,688] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:00,691] [INFO] DFAST_QC result json was written to GCF_012272835.1_ASM1227283v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:00,692] [INFO] DFAST_QC completed!
[2024-01-24 13:19:00,692] [INFO] Total running time: 0h1m27s