[2023-06-19 04:28:29,823] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:28:29,826] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:28:29,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference
[2023-06-19 04:28:31,507] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:28:31,508] [INFO] Task started: Prodigal
[2023-06-19 04:28:31,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ca64a2d-c0d7-4347-b5fd-bcf39cc1547a/GCA_018433835.1_SM3_genomic.fna.gz | prodigal -d GCA_018433835.1_SM3_genomic.fna/cds.fna -a GCA_018433835.1_SM3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:28:39,379] [INFO] Task succeeded: Prodigal
[2023-06-19 04:28:39,379] [INFO] Task started: HMMsearch
[2023-06-19 04:28:39,380] [INFO] Running command: hmmsearch --tblout GCA_018433835.1_SM3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference/reference_markers.hmm GCA_018433835.1_SM3_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:28:39,639] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:28:39,640] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0ca64a2d-c0d7-4347-b5fd-bcf39cc1547a/GCA_018433835.1_SM3_genomic.fna.gz]
[2023-06-19 04:28:39,677] [INFO] Query marker FASTA was written to GCA_018433835.1_SM3_genomic.fna/markers.fasta
[2023-06-19 04:28:39,677] [INFO] Task started: Blastn
[2023-06-19 04:28:39,678] [INFO] Running command: blastn -query GCA_018433835.1_SM3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference/reference_markers.fasta -out GCA_018433835.1_SM3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:28:40,218] [INFO] Task succeeded: Blastn
[2023-06-19 04:28:40,222] [INFO] Selected 6 target genomes.
[2023-06-19 04:28:40,222] [INFO] Target genome list was writen to GCA_018433835.1_SM3_genomic.fna/target_genomes.txt
[2023-06-19 04:28:40,232] [INFO] Task started: fastANI
[2023-06-19 04:28:40,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ca64a2d-c0d7-4347-b5fd-bcf39cc1547a/GCA_018433835.1_SM3_genomic.fna.gz --refList GCA_018433835.1_SM3_genomic.fna/target_genomes.txt --output GCA_018433835.1_SM3_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:28:44,686] [INFO] Task succeeded: fastANI
[2023-06-19 04:28:44,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:28:44,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:28:44,695] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:28:44,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 04:28:44,696] [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
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	87.7664	680	945	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	87.6481	672	945	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	87.0309	640	945	95	below_threshold
Methanoculleus chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	86.9917	655	945	95	below_threshold
Methanoculleus chikugoensis	strain=JCM 10825	GCA_001315965.1	118126	118126	type	True	86.2027	542	945	95	below_threshold
Methanoculleus bourgensis	strain=MS2T	GCA_000304355.2	83986	83986	type	True	84.1866	619	945	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 04:28:44,700] [INFO] DFAST Taxonomy check result was written to GCA_018433835.1_SM3_genomic.fna/tc_result.tsv
[2023-06-19 04:28:44,701] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:28:44,701] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:28:44,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference/checkm_data
[2023-06-19 04:28:44,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:28:44,741] [INFO] Task started: CheckM
[2023-06-19 04:28:44,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018433835.1_SM3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018433835.1_SM3_genomic.fna/checkm_input GCA_018433835.1_SM3_genomic.fna/checkm_result
[2023-06-19 04:29:13,948] [INFO] Task succeeded: CheckM
[2023-06-19 04:29:13,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:29:13,979] [INFO] ===== Completeness check finished =====
[2023-06-19 04:29:13,979] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:29:13,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018433835.1_SM3_genomic.fna/markers.fasta)
[2023-06-19 04:29:13,980] [INFO] Task started: Blastn
[2023-06-19 04:29:13,980] [INFO] Running command: blastn -query GCA_018433835.1_SM3_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd05d098-0417-4590-bb2a-87f91f459b67/dqc_reference/reference_markers_gtdb.fasta -out GCA_018433835.1_SM3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:14,453] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:14,457] [INFO] Selected 8 target genomes.
[2023-06-19 04:29:14,457] [INFO] Target genome list was writen to GCA_018433835.1_SM3_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:29:14,460] [INFO] Task started: fastANI
[2023-06-19 04:29:14,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ca64a2d-c0d7-4347-b5fd-bcf39cc1547a/GCA_018433835.1_SM3_genomic.fna.gz --refList GCA_018433835.1_SM3_genomic.fna/target_genomes_gtdb.txt --output GCA_018433835.1_SM3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:29:20,145] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:20,158] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:29:20,159] [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_018433835.1	s__Methanoculleus sp018433835	100.0	944	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.52	99.38	0.94	0.92	3	conclusive
GCA_016841955.1	s__Methanoculleus sp016841955	91.7319	671	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.79	99.79	0.97	0.97	2	-
GCA_002498065.1	s__Methanoculleus sp002498065	91.149	636	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503885.1	s__Methanoculleus marisnigri_B	88.7245	620	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	98.96	97.72	0.91	0.85	6	-
GCA_002839575.1	s__Methanoculleus sp002839575	88.0767	570	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015825.1	s__Methanoculleus marisnigri	87.779	679	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001017125.1	s__Methanoculleus sediminis	87.6329	673	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001315965.1	s__Methanoculleus chikugoensis	86.203	542	945	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:29:20,161] [INFO] GTDB search result was written to GCA_018433835.1_SM3_genomic.fna/result_gtdb.tsv
[2023-06-19 04:29:20,161] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:29:20,164] [INFO] DFAST_QC result json was written to GCA_018433835.1_SM3_genomic.fna/dqc_result.json
[2023-06-19 04:29:20,164] [INFO] DFAST_QC completed!
[2023-06-19 04:29:20,164] [INFO] Total running time: 0h0m50s