[2023-06-29 00:19:31,659] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:19:31,662] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:19:31,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference
[2023-06-29 00:19:32,883] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:19:32,884] [INFO] Task started: Prodigal
[2023-06-29 00:19:32,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg09836ffc-655c-4711-aac5-3152dd189346/GCA_017541535.1_ASM1754153v1_genomic.fna.gz | prodigal -d GCA_017541535.1_ASM1754153v1_genomic.fna/cds.fna -a GCA_017541535.1_ASM1754153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:19:42,424] [INFO] Task succeeded: Prodigal
[2023-06-29 00:19:42,425] [INFO] Task started: HMMsearch
[2023-06-29 00:19:42,425] [INFO] Running command: hmmsearch --tblout GCA_017541535.1_ASM1754153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference/reference_markers.hmm GCA_017541535.1_ASM1754153v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:19:42,716] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:19:42,718] [INFO] Found 6/6 markers.
[2023-06-29 00:19:42,753] [INFO] Query marker FASTA was written to GCA_017541535.1_ASM1754153v1_genomic.fna/markers.fasta
[2023-06-29 00:19:42,754] [INFO] Task started: Blastn
[2023-06-29 00:19:42,754] [INFO] Running command: blastn -query GCA_017541535.1_ASM1754153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference/reference_markers.fasta -out GCA_017541535.1_ASM1754153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:19:43,385] [INFO] Task succeeded: Blastn
[2023-06-29 00:19:43,389] [INFO] Selected 27 target genomes.
[2023-06-29 00:19:43,390] [INFO] Target genome list was writen to GCA_017541535.1_ASM1754153v1_genomic.fna/target_genomes.txt
[2023-06-29 00:19:43,395] [INFO] Task started: fastANI
[2023-06-29 00:19:43,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg09836ffc-655c-4711-aac5-3152dd189346/GCA_017541535.1_ASM1754153v1_genomic.fna.gz --refList GCA_017541535.1_ASM1754153v1_genomic.fna/target_genomes.txt --output GCA_017541535.1_ASM1754153v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:19:59,066] [INFO] Task succeeded: fastANI
[2023-06-29 00:19:59,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:19:59,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:19:59,071] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:19:59,071] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:19:59,071] [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
--------------------------------------------------------------------------------
[2023-06-29 00:19:59,074] [INFO] DFAST Taxonomy check result was written to GCA_017541535.1_ASM1754153v1_genomic.fna/tc_result.tsv
[2023-06-29 00:19:59,074] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:19:59,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:19:59,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference/checkm_data
[2023-06-29 00:19:59,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:19:59,121] [INFO] Task started: CheckM
[2023-06-29 00:19:59,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017541535.1_ASM1754153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017541535.1_ASM1754153v1_genomic.fna/checkm_input GCA_017541535.1_ASM1754153v1_genomic.fna/checkm_result
[2023-06-29 00:20:32,480] [INFO] Task succeeded: CheckM
[2023-06-29 00:20:32,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:20:32,505] [INFO] ===== Completeness check finished =====
[2023-06-29 00:20:32,506] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:20:32,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017541535.1_ASM1754153v1_genomic.fna/markers.fasta)
[2023-06-29 00:20:32,506] [INFO] Task started: Blastn
[2023-06-29 00:20:32,507] [INFO] Running command: blastn -query GCA_017541535.1_ASM1754153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dbdca59-e076-43cf-93f9-09c65fbfaa55/dqc_reference/reference_markers_gtdb.fasta -out GCA_017541535.1_ASM1754153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:20:33,548] [INFO] Task succeeded: Blastn
[2023-06-29 00:20:33,554] [INFO] Selected 12 target genomes.
[2023-06-29 00:20:33,554] [INFO] Target genome list was writen to GCA_017541535.1_ASM1754153v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:20:33,561] [INFO] Task started: fastANI
[2023-06-29 00:20:33,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg09836ffc-655c-4711-aac5-3152dd189346/GCA_017541535.1_ASM1754153v1_genomic.fna.gz --refList GCA_017541535.1_ASM1754153v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017541535.1_ASM1754153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:20:41,464] [INFO] Task succeeded: fastANI
[2023-06-29 00:20:41,484] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:20:41,485] [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_017527205.1	s__Acetatifactor sp017527205	98.4481	1072	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.89	95.83	0.86	0.78	5	conclusive
GCA_015056795.1	s__Acetatifactor sp015056795	89.9186	935	1204	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_017400965.1	s__Acetatifactor sp017400965	81.3457	367	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.43	98.28	0.80	0.76	3	-
GCA_017552985.1	s__Acetatifactor sp017552985	80.7599	519	1204	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	79.782	377	1204	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_016290775.1	s__Acetatifactor sp016290775	79.7636	422	1204	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_902766425.1	s__Acetatifactor sp902766425	78.0554	208	1204	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_011959105.1	s__Acetatifactor sp011959105	77.1154	53	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.00	99.00	0.85	0.85	2	-
GCA_019114005.1	s__Acetatifactor stercoripullorum	76.4893	71	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.97	99.97	0.97	0.97	2	-
GCA_017478245.1	s__Acetatifactor sp017478245	76.4862	72	1204	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_018384375.1	s__CAG-95 sp018384375	76.3653	56	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.73	98.22	0.80	0.77	3	-
--------------------------------------------------------------------------------
[2023-06-29 00:20:41,487] [INFO] GTDB search result was written to GCA_017541535.1_ASM1754153v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:20:41,488] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:20:41,491] [INFO] DFAST_QC result json was written to GCA_017541535.1_ASM1754153v1_genomic.fna/dqc_result.json
[2023-06-29 00:20:41,491] [INFO] DFAST_QC completed!
[2023-06-29 00:20:41,491] [INFO] Total running time: 0h1m10s