[2024-01-25 20:06:35,535] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:35,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:35,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference
[2024-01-25 20:06:36,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:36,722] [INFO] Task started: Prodigal
[2024-01-25 20:06:36,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc86b4ef-12d7-43c2-8d06-2c411dcb9628/GCF_025950095.1_ASM2595009v1_genomic.fna.gz | prodigal -d GCF_025950095.1_ASM2595009v1_genomic.fna/cds.fna -a GCF_025950095.1_ASM2595009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:08,804] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:08,804] [INFO] Task started: HMMsearch
[2024-01-25 20:07:08,804] [INFO] Running command: hmmsearch --tblout GCF_025950095.1_ASM2595009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference/reference_markers.hmm GCF_025950095.1_ASM2595009v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:09,105] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:09,106] [INFO] Found 6/6 markers.
[2024-01-25 20:07:09,153] [INFO] Query marker FASTA was written to GCF_025950095.1_ASM2595009v1_genomic.fna/markers.fasta
[2024-01-25 20:07:09,153] [INFO] Task started: Blastn
[2024-01-25 20:07:09,153] [INFO] Running command: blastn -query GCF_025950095.1_ASM2595009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference/reference_markers.fasta -out GCF_025950095.1_ASM2595009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:09,718] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:09,720] [INFO] Selected 14 target genomes.
[2024-01-25 20:07:09,720] [INFO] Target genome list was writen to GCF_025950095.1_ASM2595009v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:09,729] [INFO] Task started: fastANI
[2024-01-25 20:07:09,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc86b4ef-12d7-43c2-8d06-2c411dcb9628/GCF_025950095.1_ASM2595009v1_genomic.fna.gz --refList GCF_025950095.1_ASM2595009v1_genomic.fna/target_genomes.txt --output GCF_025950095.1_ASM2595009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:22,437] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:22,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:22,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:22,444] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:07:22,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:07:22,445] [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
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	79.8862	932	2061	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	78.3496	415	2061	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.5445	290	2061	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	77.2947	141	2061	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.1066	247	2061	95	below_threshold
Sulfuriroseicoccus oceanibius	strain=T37	GCA_010681825.2	2707525	2707525	type	True	76.6216	69	2061	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.3042	114	2061	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	75.9877	124	2061	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:22,446] [INFO] DFAST Taxonomy check result was written to GCF_025950095.1_ASM2595009v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:22,446] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:22,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:22,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference/checkm_data
[2024-01-25 20:07:22,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:22,506] [INFO] Task started: CheckM
[2024-01-25 20:07:22,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025950095.1_ASM2595009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025950095.1_ASM2595009v1_genomic.fna/checkm_input GCF_025950095.1_ASM2595009v1_genomic.fna/checkm_result
[2024-01-25 20:08:45,103] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:45,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:45,121] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:45,121] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:45,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025950095.1_ASM2595009v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:45,123] [INFO] Task started: Blastn
[2024-01-25 20:08:45,123] [INFO] Running command: blastn -query GCF_025950095.1_ASM2595009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83094d6b-414b-4216-81ee-10e09fc517d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_025950095.1_ASM2595009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:45,996] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:45,999] [INFO] Selected 15 target genomes.
[2024-01-25 20:08:45,999] [INFO] Target genome list was writen to GCF_025950095.1_ASM2595009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:46,019] [INFO] Task started: fastANI
[2024-01-25 20:08:46,019] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc86b4ef-12d7-43c2-8d06-2c411dcb9628/GCF_025950095.1_ASM2595009v1_genomic.fna.gz --refList GCF_025950095.1_ASM2595009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025950095.1_ASM2595009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:58,935] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:58,943] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:08:58,943] [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
GCA_000739615.1	s__Haloferula sp000739615	80.2311	1075	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	79.9042	928	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	78.9131	443	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	78.8195	666	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	78.379	412	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293445.1	s__Haloferula sp004293445	78.3237	361	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	99.99	99.98	0.97	0.96	4	-
GCA_018402445.1	s__Luteolibacter sp018402445	77.334	182	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595525.1	s__Haloferula rosea	77.1066	247	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934285.1	s__Luteolibacter sp903934285	76.4113	125	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.86	99.86	0.92	0.92	3	-
GCA_903826205.1	s__Luteolibacter sp903826205	76.2029	114	2061	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.67	99.65	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:58,944] [INFO] GTDB search result was written to GCF_025950095.1_ASM2595009v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:58,945] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:58,947] [INFO] DFAST_QC result json was written to GCF_025950095.1_ASM2595009v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:58,948] [INFO] DFAST_QC completed!
[2024-01-25 20:08:58,948] [INFO] Total running time: 0h2m23s