[2024-01-25 20:07:50,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:50,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:50,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference
[2024-01-25 20:07:51,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:51,728] [INFO] Task started: Prodigal
[2024-01-25 20:07:51,729] [INFO] Running command: gunzip -c /var/lib/cwl/stge2a98479-8824-46e9-8f82-b8f49567ff6d/GCF_016093295.1_ASM1609329v1_genomic.fna.gz | prodigal -d GCF_016093295.1_ASM1609329v1_genomic.fna/cds.fna -a GCF_016093295.1_ASM1609329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:02,732] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:02,732] [INFO] Task started: HMMsearch
[2024-01-25 20:08:02,733] [INFO] Running command: hmmsearch --tblout GCF_016093295.1_ASM1609329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference/reference_markers.hmm GCF_016093295.1_ASM1609329v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:02,958] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:02,959] [INFO] Found 6/6 markers.
[2024-01-25 20:08:02,987] [INFO] Query marker FASTA was written to GCF_016093295.1_ASM1609329v1_genomic.fna/markers.fasta
[2024-01-25 20:08:02,987] [INFO] Task started: Blastn
[2024-01-25 20:08:02,987] [INFO] Running command: blastn -query GCF_016093295.1_ASM1609329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference/reference_markers.fasta -out GCF_016093295.1_ASM1609329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:03,864] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:03,867] [INFO] Selected 11 target genomes.
[2024-01-25 20:08:03,867] [INFO] Target genome list was writen to GCF_016093295.1_ASM1609329v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:03,876] [INFO] Task started: fastANI
[2024-01-25 20:08:03,876] [INFO] Running command: fastANI --query /var/lib/cwl/stge2a98479-8824-46e9-8f82-b8f49567ff6d/GCF_016093295.1_ASM1609329v1_genomic.fna.gz --refList GCF_016093295.1_ASM1609329v1_genomic.fna/target_genomes.txt --output GCF_016093295.1_ASM1609329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:12,829] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:12,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:12,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:12,837] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:08:12,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:12,837] [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
Inhella gelatinilytica	strain=4Y10	GCA_016093295.1	2795030	2795030	type	True	100.0	1157	1161	95	conclusive
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	80.9637	658	1161	95	below_threshold
Inhella inkyongensis	strain=DSM 23958	GCA_014202795.1	392593	392593	type	True	80.6975	545	1161	95	below_threshold
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	80.635	559	1161	95	below_threshold
Inhella crocodyli	strain=CCP-18	GCA_004004565.1	2499851	2499851	type	True	79.8457	518	1161	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.7934	326	1161	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	78.2841	251	1161	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.2421	300	1161	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.0542	237	1161	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.9771	246	1161	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.7312	251	1161	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:12,839] [INFO] DFAST Taxonomy check result was written to GCF_016093295.1_ASM1609329v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:12,839] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:12,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:12,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference/checkm_data
[2024-01-25 20:08:12,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:12,879] [INFO] Task started: CheckM
[2024-01-25 20:08:12,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016093295.1_ASM1609329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016093295.1_ASM1609329v1_genomic.fna/checkm_input GCF_016093295.1_ASM1609329v1_genomic.fna/checkm_result
[2024-01-25 20:09:01,028] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:01,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:01,045] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:01,046] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:01,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016093295.1_ASM1609329v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:01,047] [INFO] Task started: Blastn
[2024-01-25 20:09:01,047] [INFO] Running command: blastn -query GCF_016093295.1_ASM1609329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdd352b7-cf2a-4649-84af-96d5c91a752d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016093295.1_ASM1609329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:02,573] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:02,576] [INFO] Selected 15 target genomes.
[2024-01-25 20:09:02,576] [INFO] Target genome list was writen to GCF_016093295.1_ASM1609329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:02,636] [INFO] Task started: fastANI
[2024-01-25 20:09:02,636] [INFO] Running command: fastANI --query /var/lib/cwl/stge2a98479-8824-46e9-8f82-b8f49567ff6d/GCF_016093295.1_ASM1609329v1_genomic.fna.gz --refList GCF_016093295.1_ASM1609329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016093295.1_ASM1609329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:14,141] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:14,150] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:14,150] [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_016093295.1	s__Inhella gelatinilytica	100.0	1157	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016093275.1	s__Inhella proteolytica	80.9714	657	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005952805.1	s__Inhella inkyongensis	80.635	559	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004004565.1	s__Inhella crocodyli	79.8228	521	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302655.1	s__Inhella sp017302655	79.3755	427	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362405.1	s__Kinneretia asaccharophila	78.9679	360	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333615.1	s__Ideonella sp000333615	78.7585	272	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015624425.1	s__Kinneretia sp015624425	78.5928	383	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113225.1	s__Mitsuaria sp900113225	78.5684	346	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	78.355	261	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_001477625.1	s__Paucibacter_A sp001477625	78.3486	324	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	78.3137	249	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768065.1	s__Aquabacterium sp000768065	78.224	241	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963075.1	s__Pelomonas sp003963075	78.2228	324	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	96.90	96.90	0.86	0.86	2	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	77.8652	244	1161	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:14,152] [INFO] GTDB search result was written to GCF_016093295.1_ASM1609329v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:14,152] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:14,155] [INFO] DFAST_QC result json was written to GCF_016093295.1_ASM1609329v1_genomic.fna/dqc_result.json
[2024-01-25 20:09:14,155] [INFO] DFAST_QC completed!
[2024-01-25 20:09:14,155] [INFO] Total running time: 0h1m24s