[2023-06-28 18:20:22,269] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:20:22,272] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:20:22,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference
[2023-06-28 18:20:23,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:20:23,831] [INFO] Task started: Prodigal
[2023-06-28 18:20:23,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgacbe4897-6a07-45b6-b851-e9ced4590c03/GCA_017400965.1_ASM1740096v1_genomic.fna.gz | prodigal -d GCA_017400965.1_ASM1740096v1_genomic.fna/cds.fna -a GCA_017400965.1_ASM1740096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:20:29,549] [INFO] Task succeeded: Prodigal
[2023-06-28 18:20:29,550] [INFO] Task started: HMMsearch
[2023-06-28 18:20:29,550] [INFO] Running command: hmmsearch --tblout GCA_017400965.1_ASM1740096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference/reference_markers.hmm GCA_017400965.1_ASM1740096v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:20:29,768] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:20:29,769] [INFO] Found 6/6 markers.
[2023-06-28 18:20:29,795] [INFO] Query marker FASTA was written to GCA_017400965.1_ASM1740096v1_genomic.fna/markers.fasta
[2023-06-28 18:20:29,796] [INFO] Task started: Blastn
[2023-06-28 18:20:29,796] [INFO] Running command: blastn -query GCA_017400965.1_ASM1740096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference/reference_markers.fasta -out GCA_017400965.1_ASM1740096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:20:32,651] [INFO] Task succeeded: Blastn
[2023-06-28 18:20:32,656] [INFO] Selected 23 target genomes.
[2023-06-28 18:20:32,657] [INFO] Target genome list was writen to GCA_017400965.1_ASM1740096v1_genomic.fna/target_genomes.txt
[2023-06-28 18:20:32,714] [INFO] Task started: fastANI
[2023-06-28 18:20:32,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgacbe4897-6a07-45b6-b851-e9ced4590c03/GCA_017400965.1_ASM1740096v1_genomic.fna.gz --refList GCA_017400965.1_ASM1740096v1_genomic.fna/target_genomes.txt --output GCA_017400965.1_ASM1740096v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:20:46,882] [INFO] Task succeeded: fastANI
[2023-06-28 18:20:46,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:20:46,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:20:46,886] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:20:46,886] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:20:46,887] [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
--------------------------------------------------------------------------------
[2023-06-28 18:20:46,889] [INFO] DFAST Taxonomy check result was written to GCA_017400965.1_ASM1740096v1_genomic.fna/tc_result.tsv
[2023-06-28 18:20:46,890] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:20:46,890] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:20:46,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference/checkm_data
[2023-06-28 18:20:46,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:20:46,920] [INFO] Task started: CheckM
[2023-06-28 18:20:46,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017400965.1_ASM1740096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017400965.1_ASM1740096v1_genomic.fna/checkm_input GCA_017400965.1_ASM1740096v1_genomic.fna/checkm_result
[2023-06-28 18:21:09,688] [INFO] Task succeeded: CheckM
[2023-06-28 18:21:09,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:21:09,708] [INFO] ===== Completeness check finished =====
[2023-06-28 18:21:09,708] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:21:09,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017400965.1_ASM1740096v1_genomic.fna/markers.fasta)
[2023-06-28 18:21:09,709] [INFO] Task started: Blastn
[2023-06-28 18:21:09,709] [INFO] Running command: blastn -query GCA_017400965.1_ASM1740096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0662ce37-d543-4271-b957-245bb26719ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_017400965.1_ASM1740096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:21:10,838] [INFO] Task succeeded: Blastn
[2023-06-28 18:21:10,842] [INFO] Selected 13 target genomes.
[2023-06-28 18:21:10,843] [INFO] Target genome list was writen to GCA_017400965.1_ASM1740096v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:21:10,879] [INFO] Task started: fastANI
[2023-06-28 18:21:10,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgacbe4897-6a07-45b6-b851-e9ced4590c03/GCA_017400965.1_ASM1740096v1_genomic.fna.gz --refList GCA_017400965.1_ASM1740096v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017400965.1_ASM1740096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:21:18,649] [INFO] Task succeeded: fastANI
[2023-06-28 18:21:18,658] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:21:18,658] [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_017400965.1	s__Acetatifactor sp017400965	100.0	645	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.43	98.28	0.80	0.76	3	conclusive
GCA_017527205.1	s__Acetatifactor sp017527205	81.2244	381	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.89	95.83	0.86	0.78	5	-
GCA_015056795.1	s__Acetatifactor sp015056795	80.8435	372	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290775.1	s__Acetatifactor sp016290775	80.818	367	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.79	96.42	0.91	0.89	5	-
GCA_017552985.1	s__Acetatifactor sp017552985	80.4823	377	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320485.1	s__Acetatifactor sp900320485	79.6221	261	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.34	98.92	0.92	0.92	3	-
GCA_017476665.1	s__Acetatifactor sp017476665	77.5448	77	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695995.1	s__Acetatifactor intestinalis	77.2878	81	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	-
GCA_002431915.1	s__Acetatifactor sp002431915	77.1368	81	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584375.1	s__Acetatifactor sp910584375	76.3732	65	655	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:21:18,660] [INFO] GTDB search result was written to GCA_017400965.1_ASM1740096v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:21:18,661] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:21:18,665] [INFO] DFAST_QC result json was written to GCA_017400965.1_ASM1740096v1_genomic.fna/dqc_result.json
[2023-06-28 18:21:18,665] [INFO] DFAST_QC completed!
[2023-06-28 18:21:18,665] [INFO] Total running time: 0h0m56s