[2024-01-24 12:23:35,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,696] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference
[2024-01-24 12:23:36,979] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:36,980] [INFO] Task started: Prodigal
[2024-01-24 12:23:36,980] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b6adbed-2743-41ee-8043-8be1ec999268/GCF_002744755.1_ASM274475v1_genomic.fna.gz | prodigal -d GCF_002744755.1_ASM274475v1_genomic.fna/cds.fna -a GCF_002744755.1_ASM274475v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:54,905] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:54,906] [INFO] Task started: HMMsearch
[2024-01-24 12:23:54,906] [INFO] Running command: hmmsearch --tblout GCF_002744755.1_ASM274475v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference/reference_markers.hmm GCF_002744755.1_ASM274475v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:55,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:55,226] [INFO] Found 6/6 markers.
[2024-01-24 12:23:55,270] [INFO] Query marker FASTA was written to GCF_002744755.1_ASM274475v1_genomic.fna/markers.fasta
[2024-01-24 12:23:55,271] [INFO] Task started: Blastn
[2024-01-24 12:23:55,271] [INFO] Running command: blastn -query GCF_002744755.1_ASM274475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference/reference_markers.fasta -out GCF_002744755.1_ASM274475v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:55,889] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:55,892] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:55,892] [INFO] Target genome list was writen to GCF_002744755.1_ASM274475v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:55,913] [INFO] Task started: fastANI
[2024-01-24 12:23:55,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b6adbed-2743-41ee-8043-8be1ec999268/GCF_002744755.1_ASM274475v1_genomic.fna.gz --refList GCF_002744755.1_ASM274475v1_genomic.fna/target_genomes.txt --output GCF_002744755.1_ASM274475v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:07,818] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:07,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:07,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:07,833] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:07,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:07,833] [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 nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	100.0	1433	1435	95	conclusive
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	79.5151	492	1435	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	79.1131	477	1435	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	78.8794	513	1435	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.862	490	1435	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	78.8253	550	1435	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	78.7776	512	1435	95	below_threshold
Gramella flava	strain=JLT2011	GCA_002120265.1	1486245	1486245	type	True	77.4234	97	1435	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.5851	57	1435	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.241	67	1435	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.1127	54	1435	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.0911	56	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:07,836] [INFO] DFAST Taxonomy check result was written to GCF_002744755.1_ASM274475v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:07,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:07,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:07,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference/checkm_data
[2024-01-24 12:24:07,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:07,884] [INFO] Task started: CheckM
[2024-01-24 12:24:07,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002744755.1_ASM274475v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002744755.1_ASM274475v1_genomic.fna/checkm_input GCF_002744755.1_ASM274475v1_genomic.fna/checkm_result
[2024-01-24 12:24:59,327] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:59,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:59,351] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:59,351] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:59,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002744755.1_ASM274475v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:59,352] [INFO] Task started: Blastn
[2024-01-24 12:24:59,352] [INFO] Running command: blastn -query GCF_002744755.1_ASM274475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4415905-8c8d-4e6f-b9bf-3266ba0a2bbf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002744755.1_ASM274475v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:00,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:00,196] [INFO] Selected 15 target genomes.
[2024-01-24 12:25:00,196] [INFO] Target genome list was writen to GCF_002744755.1_ASM274475v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:00,214] [INFO] Task started: fastANI
[2024-01-24 12:25:00,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b6adbed-2743-41ee-8043-8be1ec999268/GCF_002744755.1_ASM274475v1_genomic.fna.gz --refList GCF_002744755.1_ASM274475v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002744755.1_ASM274475v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:10,940] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:10,951] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:10,951] [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_002744755.1	s__Leeuwenhoekiella nanhaiensis	100.0	1433	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	conclusive
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	83.9496	1063	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	79.525	491	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.279	580	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.8744	488	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	78.8177	551	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	78.7696	512	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	78.004	419	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109375.1	s__Aquimarina amphilecti	76.1127	54	1435	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:10,953] [INFO] GTDB search result was written to GCF_002744755.1_ASM274475v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:10,954] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:10,957] [INFO] DFAST_QC result json was written to GCF_002744755.1_ASM274475v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:10,957] [INFO] DFAST_QC completed!
[2024-01-24 12:25:10,957] [INFO] Total running time: 0h1m35s