[2024-01-25 20:22:05,634] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:05,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:05,648] [INFO] DQC Reference Directory: /var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference
[2024-01-25 20:22:06,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:06,795] [INFO] Task started: Prodigal
[2024-01-25 20:22:06,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg19ffc3fa-88b5-478d-9004-dd46d7975f85/GCF_014337255.1_ASM1433725v1_genomic.fna.gz | prodigal -d GCF_014337255.1_ASM1433725v1_genomic.fna/cds.fna -a GCF_014337255.1_ASM1433725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:09,694] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:09,694] [INFO] Task started: HMMsearch
[2024-01-25 20:22:09,694] [INFO] Running command: hmmsearch --tblout GCF_014337255.1_ASM1433725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference/reference_markers.hmm GCF_014337255.1_ASM1433725v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:09,928] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:09,929] [INFO] Found 6/6 markers.
[2024-01-25 20:22:09,948] [INFO] Query marker FASTA was written to GCF_014337255.1_ASM1433725v1_genomic.fna/markers.fasta
[2024-01-25 20:22:09,949] [INFO] Task started: Blastn
[2024-01-25 20:22:09,949] [INFO] Running command: blastn -query GCF_014337255.1_ASM1433725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference/reference_markers.fasta -out GCF_014337255.1_ASM1433725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:10,476] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:10,481] [INFO] Selected 19 target genomes.
[2024-01-25 20:22:10,481] [INFO] Target genome list was writen to GCF_014337255.1_ASM1433725v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:10,487] [INFO] Task started: fastANI
[2024-01-25 20:22:10,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ffc3fa-88b5-478d-9004-dd46d7975f85/GCF_014337255.1_ASM1433725v1_genomic.fna.gz --refList GCF_014337255.1_ASM1433725v1_genomic.fna/target_genomes.txt --output GCF_014337255.1_ASM1433725v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:18,866] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:18,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:18,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:18,877] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:22:18,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:22:18,877] [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
Fusobacterium necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	79.5185	282	690	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_003019675.1	861	861	type	True	78.9973	264	690	95	below_threshold
Fusobacterium varium	strain=NCTC10560	GCA_900637705.1	856	856	type	True	78.9404	279	690	95	below_threshold
Fusobacterium ulcerans	strain=ATCC 49185	GCA_000158315.2	861	861	type	True	78.5564	258	690	95	below_threshold
Fusobacterium nucleatum subsp. polymorphum	strain=NCTC10562	GCA_001457555.1	76857	851	type	True	77.5388	175	690	95	below_threshold
Fusobacterium hwasookii	strain=KCOM 1249	GCA_014217355.1	1583098	1583098	type	True	77.487	168	690	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	77.4813	176	690	95	below_threshold
Fusobacterium perfoetens	strain=ATCC 29250	GCA_000622245.1	852	852	type	True	77.3416	186	690	95	below_threshold
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	77.0606	173	690	95	below_threshold
Cetobacterium somerae	strain=ATCC BAA-474	GCA_000479045.1	188913	188913	type	True	77.0261	157	690	95	below_threshold
Psychrilyobacter atlanticus	strain=DSM 19335	GCA_000426625.1	271091	271091	type	True	76.9153	87	690	95	below_threshold
Fusobacterium periodonticum	strain=ATCC 33693	GCA_000160475.1	860	860	suspected-type	True	76.7961	167	690	95	below_threshold
Fusobacterium hwasookii	strain=ChDC F128	GCA_000292935.1	1583098	1583098	type	True	76.7958	159	690	95	below_threshold
Fusobacterium russii	strain=593A	GCA_000381725.1	854	854	type	True	76.3646	105	690	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	76.0497	67	690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:18,878] [INFO] DFAST Taxonomy check result was written to GCF_014337255.1_ASM1433725v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:18,879] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:18,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:18,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference/checkm_data
[2024-01-25 20:22:18,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:18,915] [INFO] Task started: CheckM
[2024-01-25 20:22:18,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014337255.1_ASM1433725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014337255.1_ASM1433725v1_genomic.fna/checkm_input GCF_014337255.1_ASM1433725v1_genomic.fna/checkm_result
[2024-01-25 20:22:34,081] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:34,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:34,096] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:34,096] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:34,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014337255.1_ASM1433725v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:34,097] [INFO] Task started: Blastn
[2024-01-25 20:22:34,097] [INFO] Running command: blastn -query GCF_014337255.1_ASM1433725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd275b034-c860-4c47-9a92-fc14415d310f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014337255.1_ASM1433725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:34,827] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:34,831] [INFO] Selected 16 target genomes.
[2024-01-25 20:22:34,832] [INFO] Target genome list was writen to GCF_014337255.1_ASM1433725v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:34,858] [INFO] Task started: fastANI
[2024-01-25 20:22:34,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ffc3fa-88b5-478d-9004-dd46d7975f85/GCF_014337255.1_ASM1433725v1_genomic.fna.gz --refList GCF_014337255.1_ASM1433725v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014337255.1_ASM1433725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:42,723] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:42,732] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:42,733] [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_014337255.1	s__Fusobacterium_A sp900015295	100.0	688	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.50	99.45	0.93	0.92	5	conclusive
GCF_018205345.1	s__Fusobacterium_A sp018205345	81.8635	377	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.95	99.73	0.97	0.88	17	-
GCA_905193685.1	s__Fusobacterium_A sp900555485	80.132	350	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000158195.2	s__Fusobacterium_A mortiferum	79.8229	315	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.16	98.67	0.92	0.88	9	-
GCF_900450765.1	s__Fusobacterium_A necrogenes	79.5568	280	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764925.1	s__Fusobacterium_A sp900764925	79.3386	243	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003019675.1	s__Fusobacterium_A ulcerans	79.0657	262	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.20	98.24	0.93	0.85	7	-
GCA_019012925.1	s__Fusobacterium_A sp019012925	79.0651	263	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356455.1	s__Fusobacterium_A varium_A	78.8959	282	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.56	99.56	0.92	0.92	2	-
GCF_900637705.1	s__Fusobacterium_A varium	78.8774	279	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	99.17	98.59	0.93	0.87	10	-
GCF_900683735.1	s__Fusobacterium_A ulcerans_A	78.793	292	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_A	95.0	98.86	98.73	0.94	0.93	4	-
GCF_012843705.1	s__Fusobacterium_B sp012843705	77.5603	176	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984315.1	s__JAGNZR01 sp017984315	76.9724	91	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAGNZR01	95.0	99.31	99.23	0.88	0.86	3	-
GCA_016938425.1	s__JAFGUR01 sp016938425	75.8892	65	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__JAFGUR01	95.0	99.62	99.62	0.87	0.87	2	-
GCA_002342785.1	s__Psychrilyobacter sp002342785	75.6731	116	690	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Psychrilyobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:42,734] [INFO] GTDB search result was written to GCF_014337255.1_ASM1433725v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:42,734] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:42,737] [INFO] DFAST_QC result json was written to GCF_014337255.1_ASM1433725v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:42,737] [INFO] DFAST_QC completed!
[2024-01-25 20:22:42,737] [INFO] Total running time: 0h0m37s