[2024-01-24 14:19:45,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,992] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference
[2024-01-24 14:19:47,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,320] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,320] [INFO] Running command: gunzip -c /var/lib/cwl/stg331ce756-0f1b-4961-9672-bf2aa67827d5/GCF_004104055.1_ASM410405v1_genomic.fna.gz | prodigal -d GCF_004104055.1_ASM410405v1_genomic.fna/cds.fna -a GCF_004104055.1_ASM410405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:02,693] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:02,693] [INFO] Task started: HMMsearch
[2024-01-24 14:20:02,693] [INFO] Running command: hmmsearch --tblout GCF_004104055.1_ASM410405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference/reference_markers.hmm GCF_004104055.1_ASM410405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:02,962] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:02,963] [INFO] Found 6/6 markers.
[2024-01-24 14:20:03,003] [INFO] Query marker FASTA was written to GCF_004104055.1_ASM410405v1_genomic.fna/markers.fasta
[2024-01-24 14:20:03,003] [INFO] Task started: Blastn
[2024-01-24 14:20:03,003] [INFO] Running command: blastn -query GCF_004104055.1_ASM410405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference/reference_markers.fasta -out GCF_004104055.1_ASM410405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,710] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,714] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:03,714] [INFO] Target genome list was writen to GCF_004104055.1_ASM410405v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:03,720] [INFO] Task started: fastANI
[2024-01-24 14:20:03,721] [INFO] Running command: fastANI --query /var/lib/cwl/stg331ce756-0f1b-4961-9672-bf2aa67827d5/GCF_004104055.1_ASM410405v1_genomic.fna.gz --refList GCF_004104055.1_ASM410405v1_genomic.fna/target_genomes.txt --output GCF_004104055.1_ASM410405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:13,829] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:13,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:13,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:13,839] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:13,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:13,839] [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
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	100.0	1458	1460	95	conclusive
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	86.3726	1094	1460	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	86.3393	1098	1460	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	79.925	703	1460	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	79.8911	698	1460	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	79.8578	708	1460	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	78.7148	441	1460	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.6254	64	1460	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.1108	77	1460	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.9805	71	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:13,843] [INFO] DFAST Taxonomy check result was written to GCF_004104055.1_ASM410405v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:13,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:13,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:13,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference/checkm_data
[2024-01-24 14:20:13,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:13,893] [INFO] Task started: CheckM
[2024-01-24 14:20:13,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004104055.1_ASM410405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004104055.1_ASM410405v1_genomic.fna/checkm_input GCF_004104055.1_ASM410405v1_genomic.fna/checkm_result
[2024-01-24 14:21:01,757] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:01,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:01,775] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:01,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:01,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004104055.1_ASM410405v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:01,776] [INFO] Task started: Blastn
[2024-01-24 14:21:01,777] [INFO] Running command: blastn -query GCF_004104055.1_ASM410405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f85e9d-05d0-435e-a73c-4b9027f26a9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004104055.1_ASM410405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:02,742] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:02,751] [INFO] Selected 8 target genomes.
[2024-01-24 14:21:02,752] [INFO] Target genome list was writen to GCF_004104055.1_ASM410405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:02,771] [INFO] Task started: fastANI
[2024-01-24 14:21:02,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg331ce756-0f1b-4961-9672-bf2aa67827d5/GCF_004104055.1_ASM410405v1_genomic.fna.gz --refList GCF_004104055.1_ASM410405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004104055.1_ASM410405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:10,922] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:10,930] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:10,931] [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_004104055.1	s__Leeuwenhoekiella aestuarii	100.0	1458	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	conclusive
GCF_004104075.1	s__Leeuwenhoekiella polynyae	94.5591	1243	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	86.3729	1094	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	81.9397	610	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	79.9223	702	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	79.8723	706	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	79.1091	567	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	78.7148	441	1460	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:10,933] [INFO] GTDB search result was written to GCF_004104055.1_ASM410405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:10,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:10,937] [INFO] DFAST_QC result json was written to GCF_004104055.1_ASM410405v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:10,938] [INFO] DFAST_QC completed!
[2024-01-24 14:21:10,938] [INFO] Total running time: 0h1m25s