[2024-01-24 14:03:04,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:04,959] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:04,959] [INFO] DQC Reference Directory: /var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference
[2024-01-24 14:03:06,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:06,211] [INFO] Task started: Prodigal
[2024-01-24 14:03:06,211] [INFO] Running command: gunzip -c /var/lib/cwl/stgae01ad9b-13d7-46c2-ba65-21d1624f197b/GCF_013404595.1_ASM1340459v1_genomic.fna.gz | prodigal -d GCF_013404595.1_ASM1340459v1_genomic.fna/cds.fna -a GCF_013404595.1_ASM1340459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:17,117] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:17,117] [INFO] Task started: HMMsearch
[2024-01-24 14:03:17,117] [INFO] Running command: hmmsearch --tblout GCF_013404595.1_ASM1340459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference/reference_markers.hmm GCF_013404595.1_ASM1340459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:17,449] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:17,450] [INFO] Found 6/6 markers.
[2024-01-24 14:03:17,486] [INFO] Query marker FASTA was written to GCF_013404595.1_ASM1340459v1_genomic.fna/markers.fasta
[2024-01-24 14:03:17,486] [INFO] Task started: Blastn
[2024-01-24 14:03:17,486] [INFO] Running command: blastn -query GCF_013404595.1_ASM1340459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference/reference_markers.fasta -out GCF_013404595.1_ASM1340459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:18,563] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:18,567] [INFO] Selected 16 target genomes.
[2024-01-24 14:03:18,567] [INFO] Target genome list was writen to GCF_013404595.1_ASM1340459v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:18,583] [INFO] Task started: fastANI
[2024-01-24 14:03:18,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgae01ad9b-13d7-46c2-ba65-21d1624f197b/GCF_013404595.1_ASM1340459v1_genomic.fna.gz --refList GCF_013404595.1_ASM1340459v1_genomic.fna/target_genomes.txt --output GCF_013404595.1_ASM1340459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:30,320] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:30,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:30,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:30,335] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:30,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:30,335] [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
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	100.0	1256	1257	95	conclusive
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	80.3548	710	1257	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.9548	644	1257	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.9274	640	1257	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	79.7734	697	1257	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	79.267	660	1257	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.3769	484	1257	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.2538	403	1257	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.2272	406	1257	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.2164	450	1257	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.1025	369	1257	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.0315	373	1257	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.9487	376	1257	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7968	345	1257	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6993	350	1257	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5967	331	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:30,337] [INFO] DFAST Taxonomy check result was written to GCF_013404595.1_ASM1340459v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:30,338] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:30,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:30,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference/checkm_data
[2024-01-24 14:03:30,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:30,384] [INFO] Task started: CheckM
[2024-01-24 14:03:30,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013404595.1_ASM1340459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013404595.1_ASM1340459v1_genomic.fna/checkm_input GCF_013404595.1_ASM1340459v1_genomic.fna/checkm_result
[2024-01-24 14:04:06,574] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:06,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:06,596] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:06,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:06,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013404595.1_ASM1340459v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:06,597] [INFO] Task started: Blastn
[2024-01-24 14:04:06,597] [INFO] Running command: blastn -query GCF_013404595.1_ASM1340459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge037e1c5-1617-4552-a797-f41265809309/dqc_reference/reference_markers_gtdb.fasta -out GCF_013404595.1_ASM1340459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:08,503] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:08,508] [INFO] Selected 13 target genomes.
[2024-01-24 14:04:08,508] [INFO] Target genome list was writen to GCF_013404595.1_ASM1340459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:08,593] [INFO] Task started: fastANI
[2024-01-24 14:04:08,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgae01ad9b-13d7-46c2-ba65-21d1624f197b/GCF_013404595.1_ASM1340459v1_genomic.fna.gz --refList GCF_013404595.1_ASM1340459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013404595.1_ASM1340459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:18,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:19,008] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:19,009] [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_013404595.1	s__Jannaschia marina	100.0	1255	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003340555.1	s__Jannaschia formosa	80.3828	707	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403795.1	s__Jannaschia donghaensis	80.1278	734	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.9104	642	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113875.1	s__Jannaschia pohangensis	79.7583	699	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	79.5012	622	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016820245.1	s__Jannaschia sp016820245	79.4263	626	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	79.323	504	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	79.2527	662	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.3408	479	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.2441	404	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.2168	450	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.9174	378	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:19,012] [INFO] GTDB search result was written to GCF_013404595.1_ASM1340459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:19,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:19,017] [INFO] DFAST_QC result json was written to GCF_013404595.1_ASM1340459v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:19,017] [INFO] DFAST_QC completed!
[2024-01-24 14:04:19,017] [INFO] Total running time: 0h1m14s