[2024-01-24 13:40:35,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,136] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,136] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference
[2024-01-24 13:40:36,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,456] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,456] [INFO] Running command: gunzip -c /var/lib/cwl/stga605e9b8-0d82-4096-acdc-2f16d3327be8/GCF_004331645.1_ASM433164v1_genomic.fna.gz | prodigal -d GCF_004331645.1_ASM433164v1_genomic.fna/cds.fna -a GCF_004331645.1_ASM433164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,113] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,113] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,113] [INFO] Running command: hmmsearch --tblout GCF_004331645.1_ASM433164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference/reference_markers.hmm GCF_004331645.1_ASM433164v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,481] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,536] [INFO] Query marker FASTA was written to GCF_004331645.1_ASM433164v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,537] [INFO] Task started: Blastn
[2024-01-24 13:40:58,537] [INFO] Running command: blastn -query GCF_004331645.1_ASM433164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference/reference_markers.fasta -out GCF_004331645.1_ASM433164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,190] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,194] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:59,195] [INFO] Target genome list was writen to GCF_004331645.1_ASM433164v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,207] [INFO] Task started: fastANI
[2024-01-24 13:40:59,208] [INFO] Running command: fastANI --query /var/lib/cwl/stga605e9b8-0d82-4096-acdc-2f16d3327be8/GCF_004331645.1_ASM433164v1_genomic.fna.gz --refList GCF_004331645.1_ASM433164v1_genomic.fna/target_genomes.txt --output GCF_004331645.1_ASM433164v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:12,379] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:12,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:12,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:12,392] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:12,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:12,393] [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
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	100.0	1929	1929	95	conclusive
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	81.6161	913	1929	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	81.0618	747	1929	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	80.2978	729	1929	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	79.0885	533	1929	95	below_threshold
Pedobacter insulae	strain=DSM 18684	GCA_900113525.1	414048	414048	type	True	78.5285	448	1929	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	77.9993	352	1929	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	77.9632	358	1929	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	77.8979	187	1929	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.8793	360	1929	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.4233	274	1929	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.8748	67	1929	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.4673	148	1929	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	76.0795	92	1929	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:12,394] [INFO] DFAST Taxonomy check result was written to GCF_004331645.1_ASM433164v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:12,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:12,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:12,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference/checkm_data
[2024-01-24 13:41:12,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:12,454] [INFO] Task started: CheckM
[2024-01-24 13:41:12,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331645.1_ASM433164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331645.1_ASM433164v1_genomic.fna/checkm_input GCF_004331645.1_ASM433164v1_genomic.fna/checkm_result
[2024-01-24 13:42:13,581] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:13,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,605] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:13,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:13,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331645.1_ASM433164v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:13,606] [INFO] Task started: Blastn
[2024-01-24 13:42:13,606] [INFO] Running command: blastn -query GCF_004331645.1_ASM433164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb60b71c-a87c-48df-8f95-6284103d0223/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331645.1_ASM433164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:14,498] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:14,512] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:14,512] [INFO] Target genome list was writen to GCF_004331645.1_ASM433164v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:14,519] [INFO] Task started: fastANI
[2024-01-24 13:42:14,520] [INFO] Running command: fastANI --query /var/lib/cwl/stga605e9b8-0d82-4096-acdc-2f16d3327be8/GCF_004331645.1_ASM433164v1_genomic.fna.gz --refList GCF_004331645.1_ASM433164v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331645.1_ASM433164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:23,303] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:23,314] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:23,314] [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_004331645.1	s__Pedobacter sp004331645	100.0	1929	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004295885.1	s__Pedobacter sp004295885	85.3359	772	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	81.6209	913	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	81.0733	747	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204825.1	s__Pedobacter boryungensis	80.6488	694	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116475.1	s__Pedobacter sp005116475	80.2896	730	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412215.1	s__Pedobacter sp001412215	79.7024	622	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054115.1	s__Pedobacter sp003054115	78.1937	237	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635725.1	s__Pedobacter mendelii	77.5522	298	1929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:23,316] [INFO] GTDB search result was written to GCF_004331645.1_ASM433164v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:23,316] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:23,320] [INFO] DFAST_QC result json was written to GCF_004331645.1_ASM433164v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:23,320] [INFO] DFAST_QC completed!
[2024-01-24 13:42:23,320] [INFO] Total running time: 0h1m48s