[2023-06-19 06:44:51,550] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:44:51,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:44:51,554] [INFO] DQC Reference Directory: /var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference
[2023-06-19 06:44:53,982] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:44:53,983] [INFO] Task started: Prodigal
[2023-06-19 06:44:53,983] [INFO] Running command: gunzip -c /var/lib/cwl/stgecf30d6d-aebd-45f5-b34f-20a6f5312032/GCA_013415585.1_ASM1341558v1_genomic.fna.gz | prodigal -d GCA_013415585.1_ASM1341558v1_genomic.fna/cds.fna -a GCA_013415585.1_ASM1341558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:44:56,972] [INFO] Task succeeded: Prodigal
[2023-06-19 06:44:56,973] [INFO] Task started: HMMsearch
[2023-06-19 06:44:56,973] [INFO] Running command: hmmsearch --tblout GCA_013415585.1_ASM1341558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference/reference_markers.hmm GCA_013415585.1_ASM1341558v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:44:57,207] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:44:57,209] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgecf30d6d-aebd-45f5-b34f-20a6f5312032/GCA_013415585.1_ASM1341558v1_genomic.fna.gz]
[2023-06-19 06:44:57,230] [INFO] Query marker FASTA was written to GCA_013415585.1_ASM1341558v1_genomic.fna/markers.fasta
[2023-06-19 06:44:57,230] [INFO] Task started: Blastn
[2023-06-19 06:44:57,230] [INFO] Running command: blastn -query GCA_013415585.1_ASM1341558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference/reference_markers.fasta -out GCA_013415585.1_ASM1341558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:44:58,918] [INFO] Task succeeded: Blastn
[2023-06-19 06:44:58,923] [INFO] Selected 5 target genomes.
[2023-06-19 06:44:58,923] [INFO] Target genome list was writen to GCA_013415585.1_ASM1341558v1_genomic.fna/target_genomes.txt
[2023-06-19 06:44:58,925] [INFO] Task started: fastANI
[2023-06-19 06:44:58,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgecf30d6d-aebd-45f5-b34f-20a6f5312032/GCA_013415585.1_ASM1341558v1_genomic.fna.gz --refList GCA_013415585.1_ASM1341558v1_genomic.fna/target_genomes.txt --output GCA_013415585.1_ASM1341558v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:45:01,000] [INFO] Task succeeded: fastANI
[2023-06-19 06:45:01,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:45:01,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:45:01,014] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:45:01,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:45:01,014] [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
Methanococcoides vulcani	strain=SLH 33	GCA_900111645.1	1353158	1353158	type	True	89.1509	260	287	95	below_threshold
Methanococcoides vulcani		GCA_900773955.1	1353158	1353158	type	True	89.0244	264	287	95	below_threshold
Methanococcoides orientis	strain=LMO-1	GCA_021184045.1	2822137	2822137	type	True	88.0111	269	287	95	below_threshold
Methanococcoides methylutens		GCA_900773915.1	2226	2226	type	True	87.9158	270	287	95	below_threshold
Methanococcoides methylutens	strain=DSM 2657	GCA_000765475.1	2226	2226	type	True	87.915	267	287	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:45:01,017] [INFO] DFAST Taxonomy check result was written to GCA_013415585.1_ASM1341558v1_genomic.fna/tc_result.tsv
[2023-06-19 06:45:01,017] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:45:01,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:45:01,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference/checkm_data
[2023-06-19 06:45:01,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:45:01,043] [INFO] Task started: CheckM
[2023-06-19 06:45:01,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013415585.1_ASM1341558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013415585.1_ASM1341558v1_genomic.fna/checkm_input GCA_013415585.1_ASM1341558v1_genomic.fna/checkm_result
[2023-06-19 06:45:18,538] [INFO] Task succeeded: CheckM
[2023-06-19 06:45:18,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.87%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 06:45:18,565] [INFO] ===== Completeness check finished =====
[2023-06-19 06:45:18,565] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:45:18,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013415585.1_ASM1341558v1_genomic.fna/markers.fasta)
[2023-06-19 06:45:18,565] [INFO] Task started: Blastn
[2023-06-19 06:45:18,565] [INFO] Running command: blastn -query GCA_013415585.1_ASM1341558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5fc1700-3586-4423-bb34-c8ccc26a0f6f/dqc_reference/reference_markers_gtdb.fasta -out GCA_013415585.1_ASM1341558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:45:19,007] [INFO] Task succeeded: Blastn
[2023-06-19 06:45:19,011] [INFO] Selected 5 target genomes.
[2023-06-19 06:45:19,011] [INFO] Target genome list was writen to GCA_013415585.1_ASM1341558v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:45:19,017] [INFO] Task started: fastANI
[2023-06-19 06:45:19,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgecf30d6d-aebd-45f5-b34f-20a6f5312032/GCA_013415585.1_ASM1341558v1_genomic.fna.gz --refList GCA_013415585.1_ASM1341558v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013415585.1_ASM1341558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:45:21,315] [INFO] Task succeeded: fastANI
[2023-06-19 06:45:21,326] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 06:45:21,326] [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_900111645.1	s__Methanococcoides vulcani	89.1509	260	287	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	97.94	95.89	0.92	0.84	3	-
GCF_900774055.1	s__Methanococcoides sp900774055	88.1831	265	287	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000765475.1	s__Methanococcoides methylutens	87.915	267	287	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000970325.1	s__Methanococcoides methylutens_A	83.8072	261	287	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013725.1	s__Methanococcoides burtonii	79.1913	144	287	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanococcoides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:45:21,328] [INFO] GTDB search result was written to GCA_013415585.1_ASM1341558v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:45:21,328] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:45:21,331] [INFO] DFAST_QC result json was written to GCA_013415585.1_ASM1341558v1_genomic.fna/dqc_result.json
[2023-06-19 06:45:21,331] [INFO] DFAST_QC completed!
[2023-06-19 06:45:21,331] [INFO] Total running time: 0h0m30s