[2024-01-24 12:31:58,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:58,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:58,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference
[2024-01-24 12:32:00,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:32:00,036] [INFO] Task started: Prodigal
[2024-01-24 12:32:00,036] [INFO] Running command: gunzip -c /var/lib/cwl/stg5efe606e-c4a3-4d4b-a5da-6a1e9036285d/GCF_011008935.1_ASM1100893v1_genomic.fna.gz | prodigal -d GCF_011008935.1_ASM1100893v1_genomic.fna/cds.fna -a GCF_011008935.1_ASM1100893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:12,265] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:12,266] [INFO] Task started: HMMsearch
[2024-01-24 12:32:12,266] [INFO] Running command: hmmsearch --tblout GCF_011008935.1_ASM1100893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference/reference_markers.hmm GCF_011008935.1_ASM1100893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:12,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:12,553] [INFO] Found 6/6 markers.
[2024-01-24 12:32:12,589] [INFO] Query marker FASTA was written to GCF_011008935.1_ASM1100893v1_genomic.fna/markers.fasta
[2024-01-24 12:32:12,589] [INFO] Task started: Blastn
[2024-01-24 12:32:12,589] [INFO] Running command: blastn -query GCF_011008935.1_ASM1100893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference/reference_markers.fasta -out GCF_011008935.1_ASM1100893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:13,654] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:13,658] [INFO] Selected 20 target genomes.
[2024-01-24 12:32:13,658] [INFO] Target genome list was writen to GCF_011008935.1_ASM1100893v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:13,664] [INFO] Task started: fastANI
[2024-01-24 12:32:13,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg5efe606e-c4a3-4d4b-a5da-6a1e9036285d/GCF_011008935.1_ASM1100893v1_genomic.fna.gz --refList GCF_011008935.1_ASM1100893v1_genomic.fna/target_genomes.txt --output GCF_011008935.1_ASM1100893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:31,362] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:31,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:31,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:31,378] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:32:31,379] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:32:31,379] [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
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	80.4324	659	1260	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.2321	650	1260	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	80.1566	653	1260	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.0998	657	1260	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	80.0615	665	1260	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	80.0555	566	1260	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	80.0551	638	1260	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.9624	624	1260	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	79.9504	669	1260	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.941	642	1260	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.93	641	1260	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.903	617	1260	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.8234	672	1260	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.6519	642	1260	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.6048	589	1260	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.5531	553	1260	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	79.5299	565	1260	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	79.2779	551	1260	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.2041	571	1260	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	79.1056	593	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:31,381] [INFO] DFAST Taxonomy check result was written to GCF_011008935.1_ASM1100893v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:31,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:31,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:31,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference/checkm_data
[2024-01-24 12:32:31,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:31,430] [INFO] Task started: CheckM
[2024-01-24 12:32:31,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011008935.1_ASM1100893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011008935.1_ASM1100893v1_genomic.fna/checkm_input GCF_011008935.1_ASM1100893v1_genomic.fna/checkm_result
[2024-01-24 12:33:16,914] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:16,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:16,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:16,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:16,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011008935.1_ASM1100893v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:16,941] [INFO] Task started: Blastn
[2024-01-24 12:33:16,941] [INFO] Running command: blastn -query GCF_011008935.1_ASM1100893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e5f113c-dfd4-4316-8fbd-07fd7b2fae48/dqc_reference/reference_markers_gtdb.fasta -out GCF_011008935.1_ASM1100893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:18,962] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:18,968] [INFO] Selected 18 target genomes.
[2024-01-24 12:33:18,968] [INFO] Target genome list was writen to GCF_011008935.1_ASM1100893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:18,980] [INFO] Task started: fastANI
[2024-01-24 12:33:18,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg5efe606e-c4a3-4d4b-a5da-6a1e9036285d/GCF_011008935.1_ASM1100893v1_genomic.fna.gz --refList GCF_011008935.1_ASM1100893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011008935.1_ASM1100893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:33,900] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:33,921] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:33,921] [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_011008935.1	s__KMS-5 sp011008935	100.0	1259	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016869835.1	s__KMS-5 sp016869835	82.917	675	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	81.9657	588	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328815.1	s__UBA1943 sp013328815	81.6542	772	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
GCF_011043545.1	s__JAAKGP01 sp011043545	80.9391	711	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336845.1	s__UBA1943 sp002336845	80.1792	599	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765795.1	s__UBA1943 sp016765795	80.1623	661	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011174775.1	s__Tabrizicola sp011174775	80.162	654	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	80.1161	657	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570715.1	s__Gemmobacter lutimaris	80.0708	661	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	79.9963	626	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	79.9324	643	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002855575.1	s__Gemmobacter_B sp002855575	79.8287	646	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222785.1	s__Tabrizicola sp005222785	79.7217	602	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879735.1	s__Pseudogemmobacter sp014879735	79.694	573	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	79.6589	642	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	79.5436	546	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792685.1	s__Tabrizicola sp016792685	79.436	529	1260	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:33,923] [INFO] GTDB search result was written to GCF_011008935.1_ASM1100893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:33,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:33,928] [INFO] DFAST_QC result json was written to GCF_011008935.1_ASM1100893v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:33,929] [INFO] DFAST_QC completed!
[2024-01-24 12:33:33,929] [INFO] Total running time: 0h1m35s