[2024-01-24 11:09:50,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference
[2024-01-24 11:09:53,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,304] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg37b8a7de-a99e-45b4-be3d-2e64a1a03c1f/GCF_024170505.1_ASM2417050v1_genomic.fna.gz | prodigal -d GCF_024170505.1_ASM2417050v1_genomic.fna/cds.fna -a GCF_024170505.1_ASM2417050v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:09:58,928] [INFO] Task succeeded: Prodigal
[2024-01-24 11:09:58,929] [INFO] Task started: HMMsearch
[2024-01-24 11:09:58,929] [INFO] Running command: hmmsearch --tblout GCF_024170505.1_ASM2417050v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference/reference_markers.hmm GCF_024170505.1_ASM2417050v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:09:59,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:09:59,154] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg37b8a7de-a99e-45b4-be3d-2e64a1a03c1f/GCF_024170505.1_ASM2417050v1_genomic.fna.gz]
[2024-01-24 11:09:59,179] [INFO] Query marker FASTA was written to GCF_024170505.1_ASM2417050v1_genomic.fna/markers.fasta
[2024-01-24 11:09:59,180] [INFO] Task started: Blastn
[2024-01-24 11:09:59,180] [INFO] Running command: blastn -query GCF_024170505.1_ASM2417050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference/reference_markers.fasta -out GCF_024170505.1_ASM2417050v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:00,081] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:00,085] [INFO] Selected 6 target genomes.
[2024-01-24 11:10:00,086] [INFO] Target genome list was writen to GCF_024170505.1_ASM2417050v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:00,136] [INFO] Task started: fastANI
[2024-01-24 11:10:00,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg37b8a7de-a99e-45b4-be3d-2e64a1a03c1f/GCF_024170505.1_ASM2417050v1_genomic.fna.gz --refList GCF_024170505.1_ASM2417050v1_genomic.fna/target_genomes.txt --output GCF_024170505.1_ASM2417050v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:03,054] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:03,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:03,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:03,068] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:10:03,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:03,068] [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
Methanocalculus alkaliphilus	strain=AMF2	GCA_024170505.1	768730	768730	type	True	100.0	676	678	95	conclusive
Methanocalculus chunghsingensis	strain=K1F9705b	GCA_018132105.1	156457	156457	type	True	89.1131	571	678	95	below_threshold
Methanocalculus taiwanensis	strain=P2F9704a	GCA_024372745.1	106207	106207	type	True	78.5021	259	678	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	76.586	52	678	95	below_threshold
Methanofollis ethanolicus	strain=HASU	GCA_001571385.1	488124	488124	type	True	76.284	53	678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:03,070] [INFO] DFAST Taxonomy check result was written to GCF_024170505.1_ASM2417050v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:03,071] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:03,071] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:03,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference/checkm_data
[2024-01-24 11:10:03,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:03,102] [INFO] Task started: CheckM
[2024-01-24 11:10:03,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024170505.1_ASM2417050v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024170505.1_ASM2417050v1_genomic.fna/checkm_input GCF_024170505.1_ASM2417050v1_genomic.fna/checkm_result
[2024-01-24 11:10:29,005] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:29,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:29,022] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:29,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:29,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024170505.1_ASM2417050v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:29,023] [INFO] Task started: Blastn
[2024-01-24 11:10:29,024] [INFO] Running command: blastn -query GCF_024170505.1_ASM2417050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64cd43a7-6dc9-4308-8808-3f2634b9007b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024170505.1_ASM2417050v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:29,474] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:29,476] [INFO] Selected 10 target genomes.
[2024-01-24 11:10:29,476] [INFO] Target genome list was writen to GCF_024170505.1_ASM2417050v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:29,520] [INFO] Task started: fastANI
[2024-01-24 11:10:29,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg37b8a7de-a99e-45b4-be3d-2e64a1a03c1f/GCF_024170505.1_ASM2417050v1_genomic.fna.gz --refList GCF_024170505.1_ASM2417050v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024170505.1_ASM2417050v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:10:33,338] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:33,352] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:10:33,352] [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
GCA_007130455.1	s__Methanocalculus sp007130455	98.8781	376	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018132105.1	s__Methanocalculus chunghsingensis	89.1312	570	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003838185.1	s__Methanocalculus sp003838185	78.9896	233	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	99.84	99.82	0.91	0.91	3	-
GCA_002496395.1	s__Methanocalculus sp002496395	78.8724	270	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003838065.1	s__Methanocalculus sp003838065	78.8002	153	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	99.38	99.38	0.75	0.75	2	-
GCA_013329165.1	s__Methanocalculus sp9912u	78.6498	255	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanocorpusculaceae;g__Methanocalculus	95.0	99.13	98.71	0.84	0.82	3	-
GCF_001602375.1	s__Methanoculleus horonobensis	76.586	52	678	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:10:33,354] [INFO] GTDB search result was written to GCF_024170505.1_ASM2417050v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:10:33,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:10:33,356] [INFO] DFAST_QC result json was written to GCF_024170505.1_ASM2417050v1_genomic.fna/dqc_result.json
[2024-01-24 11:10:33,357] [INFO] DFAST_QC completed!
[2024-01-24 11:10:33,357] [INFO] Total running time: 0h0m43s