[2024-01-24 13:17:48,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:48,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:48,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference
[2024-01-24 13:17:49,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:49,771] [INFO] Task started: Prodigal
[2024-01-24 13:17:49,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dea7e48-20d6-4502-a397-8727e452e180/GCF_007752135.1_ASM775213v1_genomic.fna.gz | prodigal -d GCF_007752135.1_ASM775213v1_genomic.fna/cds.fna -a GCF_007752135.1_ASM775213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:31,875] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:31,876] [INFO] Task started: HMMsearch
[2024-01-24 13:18:31,876] [INFO] Running command: hmmsearch --tblout GCF_007752135.1_ASM775213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference/reference_markers.hmm GCF_007752135.1_ASM775213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:32,361] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:32,363] [INFO] Found 6/6 markers.
[2024-01-24 13:18:32,426] [INFO] Query marker FASTA was written to GCF_007752135.1_ASM775213v1_genomic.fna/markers.fasta
[2024-01-24 13:18:32,426] [INFO] Task started: Blastn
[2024-01-24 13:18:32,426] [INFO] Running command: blastn -query GCF_007752135.1_ASM775213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference/reference_markers.fasta -out GCF_007752135.1_ASM775213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:33,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:33,022] [INFO] Selected 25 target genomes.
[2024-01-24 13:18:33,022] [INFO] Target genome list was writen to GCF_007752135.1_ASM775213v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:33,051] [INFO] Task started: fastANI
[2024-01-24 13:18:33,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dea7e48-20d6-4502-a397-8727e452e180/GCF_007752135.1_ASM775213v1_genomic.fna.gz --refList GCF_007752135.1_ASM775213v1_genomic.fna/target_genomes.txt --output GCF_007752135.1_ASM775213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:03,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:03,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:03,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:03,508] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:03,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:03,508] [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
Aureliella helgolandensis	strain=Q31a	GCA_007752135.1	2527968	2527968	type	True	100.0	2812	2813	95	conclusive
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	78.1619	68	2813	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.4344	74	2813	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	77.1742	64	2813	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	76.6529	84	2813	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.0571	81	2813	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.0509	61	2813	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	75.95	63	2813	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.9144	56	2813	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.7441	56	2813	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	75.6335	52	2813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:03,510] [INFO] DFAST Taxonomy check result was written to GCF_007752135.1_ASM775213v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:03,513] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:03,513] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:03,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference/checkm_data
[2024-01-24 13:19:03,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:03,599] [INFO] Task started: CheckM
[2024-01-24 13:19:03,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007752135.1_ASM775213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007752135.1_ASM775213v1_genomic.fna/checkm_input GCF_007752135.1_ASM775213v1_genomic.fna/checkm_result
[2024-01-24 13:20:57,124] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:57,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:57,152] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:57,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:57,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007752135.1_ASM775213v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:57,153] [INFO] Task started: Blastn
[2024-01-24 13:20:57,153] [INFO] Running command: blastn -query GCF_007752135.1_ASM775213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea456e07-7772-4344-99fd-9f6554dadc89/dqc_reference/reference_markers_gtdb.fasta -out GCF_007752135.1_ASM775213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:57,927] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:57,932] [INFO] Selected 26 target genomes.
[2024-01-24 13:20:57,932] [INFO] Target genome list was writen to GCF_007752135.1_ASM775213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:58,012] [INFO] Task started: fastANI
[2024-01-24 13:20:58,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dea7e48-20d6-4502-a397-8727e452e180/GCF_007752135.1_ASM775213v1_genomic.fna.gz --refList GCF_007752135.1_ASM775213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007752135.1_ASM775213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:24,639] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:24,651] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:24,651] [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_007752135.1	s__Aureliella helgolandensis	100.0	2812	2813	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Aureliella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001027925.1	s__Rhodopirellula islandica	77.2085	63	2813	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	76.8998	59	2813	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	76.0454	83	2813	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695565.1	s__Aureliella sp003695565	75.528	51	2813	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Aureliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367455.1	s__Laterigemmans baculatus	75.1448	59	2813	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:24,653] [INFO] GTDB search result was written to GCF_007752135.1_ASM775213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:24,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:24,656] [INFO] DFAST_QC result json was written to GCF_007752135.1_ASM775213v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:24,656] [INFO] DFAST_QC completed!
[2024-01-24 13:21:24,656] [INFO] Total running time: 0h3m36s