[2023-06-19 07:17:04,339] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:17:04,389] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:17:04,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference
[2023-06-19 07:17:06,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:17:06,562] [INFO] Task started: Prodigal
[2023-06-19 07:17:06,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg118b60ea-fc91-4376-a333-2432c02b4c65/GCA_018436255.1_R1_genomic.fna.gz | prodigal -d GCA_018436255.1_R1_genomic.fna/cds.fna -a GCA_018436255.1_R1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:17:11,572] [INFO] Task succeeded: Prodigal
[2023-06-19 07:17:11,572] [INFO] Task started: HMMsearch
[2023-06-19 07:17:11,573] [INFO] Running command: hmmsearch --tblout GCA_018436255.1_R1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference/reference_markers.hmm GCA_018436255.1_R1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:17:11,810] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:17:11,811] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg118b60ea-fc91-4376-a333-2432c02b4c65/GCA_018436255.1_R1_genomic.fna.gz]
[2023-06-19 07:17:11,840] [INFO] Query marker FASTA was written to GCA_018436255.1_R1_genomic.fna/markers.fasta
[2023-06-19 07:17:11,841] [INFO] Task started: Blastn
[2023-06-19 07:17:11,841] [INFO] Running command: blastn -query GCA_018436255.1_R1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference/reference_markers.fasta -out GCA_018436255.1_R1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:17:12,324] [INFO] Task succeeded: Blastn
[2023-06-19 07:17:12,328] [INFO] Selected 5 target genomes.
[2023-06-19 07:17:12,328] [INFO] Target genome list was writen to GCA_018436255.1_R1_genomic.fna/target_genomes.txt
[2023-06-19 07:17:12,330] [INFO] Task started: fastANI
[2023-06-19 07:17:12,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg118b60ea-fc91-4376-a333-2432c02b4c65/GCA_018436255.1_R1_genomic.fna.gz --refList GCA_018436255.1_R1_genomic.fna/target_genomes.txt --output GCA_018436255.1_R1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:17:15,026] [INFO] Task succeeded: fastANI
[2023-06-19 07:17:15,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:17:15,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:17:15,036] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:17:15,036] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:17:15,036] [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
Methanomethylovorans hollandica	strain=DSM 15978	GCA_000328665.1	101192	101192	type	True	82.1999	475	653	95	below_threshold
Methanolobus tindarius	strain=DSM 2278	GCA_000504205.1	2221	2221	type	True	76.2062	64	653	95	below_threshold
Methanolobus profundi	strain=Mob M	GCA_900114835.1	487685	487685	type	True	76.0347	70	653	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:17:15,038] [INFO] DFAST Taxonomy check result was written to GCA_018436255.1_R1_genomic.fna/tc_result.tsv
[2023-06-19 07:17:15,039] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:17:15,039] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:17:15,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference/checkm_data
[2023-06-19 07:17:15,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:17:15,067] [INFO] Task started: CheckM
[2023-06-19 07:17:15,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018436255.1_R1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018436255.1_R1_genomic.fna/checkm_input GCA_018436255.1_R1_genomic.fna/checkm_result
[2023-06-19 07:17:38,117] [INFO] Task succeeded: CheckM
[2023-06-19 07:17:38,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:17:38,136] [INFO] ===== Completeness check finished =====
[2023-06-19 07:17:38,136] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:17:38,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018436255.1_R1_genomic.fna/markers.fasta)
[2023-06-19 07:17:38,137] [INFO] Task started: Blastn
[2023-06-19 07:17:38,137] [INFO] Running command: blastn -query GCA_018436255.1_R1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96cc724b-67c9-486f-adce-206fd2767fdd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018436255.1_R1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:17:38,542] [INFO] Task succeeded: Blastn
[2023-06-19 07:17:38,547] [INFO] Selected 8 target genomes.
[2023-06-19 07:17:38,547] [INFO] Target genome list was writen to GCA_018436255.1_R1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:17:38,552] [INFO] Task started: fastANI
[2023-06-19 07:17:38,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg118b60ea-fc91-4376-a333-2432c02b4c65/GCA_018436255.1_R1_genomic.fna.gz --refList GCA_018436255.1_R1_genomic.fna/target_genomes_gtdb.txt --output GCA_018436255.1_R1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:17:42,658] [INFO] Task succeeded: fastANI
[2023-06-19 07:17:42,668] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:17:42,668] [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_001896725.1	s__Methanomethylovorans sp001896725	99.8818	626	653	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanomethylovorans	95.0	99.86	99.81	0.97	0.96	4	conclusive
GCA_002067275.1	s__Methanomethylovorans sp002067275	85.9899	456	653	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanomethylovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328665.1	s__Methanomethylovorans hollandica	82.1997	475	653	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanomethylovorans	95.0	97.56	97.48	0.95	0.95	3	-
GCA_002067265.1	s__Methanomethylovorans sp002067265	80.1674	220	653	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanomethylovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002508425.1	s__Methanomethylovorans sp002508425	79.9117	368	653	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanomethylovorans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:17:42,670] [INFO] GTDB search result was written to GCA_018436255.1_R1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:17:42,671] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:17:42,674] [INFO] DFAST_QC result json was written to GCA_018436255.1_R1_genomic.fna/dqc_result.json
[2023-06-19 07:17:42,674] [INFO] DFAST_QC completed!
[2023-06-19 07:17:42,674] [INFO] Total running time: 0h0m38s