[2023-06-08 11:15:59,882] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:15:59,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:15:59,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference
[2023-06-08 11:16:01,182] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:01,183] [INFO] Task started: Prodigal
[2023-06-08 11:16:01,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg46c54113-0350-4b62-aaab-5231287de5ad/GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:05,646] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:05,646] [INFO] Task started: HMMsearch
[2023-06-08 11:16:05,646] [INFO] Running command: hmmsearch --tblout GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference/reference_markers.hmm GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:05,897] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:05,898] [INFO] Found 6/6 markers.
[2023-06-08 11:16:05,931] [INFO] Query marker FASTA was written to GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:16:05,931] [INFO] Task started: Blastn
[2023-06-08 11:16:05,931] [INFO] Running command: blastn -query GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference/reference_markers.fasta -out GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:06,552] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:06,556] [INFO] Selected 30 target genomes.
[2023-06-08 11:16:06,556] [INFO] Target genome list was writen to GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:16:06,559] [INFO] Task started: fastANI
[2023-06-08 11:16:06,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c54113-0350-4b62-aaab-5231287de5ad/GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:16:26,251] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:26,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:16:26,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:16:26,261] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:16:26,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:16:26,262] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.6244	76	529	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.6072	59	529	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.3313	68	529	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.1737	69	529	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:16:26,264] [INFO] DFAST Taxonomy check result was written to GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:16:26,265] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:16:26,265] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:16:26,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference/checkm_data
[2023-06-08 11:16:26,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:16:26,296] [INFO] Task started: CheckM
[2023-06-08 11:16:26,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:16:47,452] [INFO] Task succeeded: CheckM
[2023-06-08 11:16:47,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:16:47,479] [INFO] ===== Completeness check finished =====
[2023-06-08 11:16:47,480] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:16:47,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:16:47,481] [INFO] Task started: Blastn
[2023-06-08 11:16:47,481] [INFO] Running command: blastn -query GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf0be884-eb1d-4608-8291-f2b12c08199d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:48,270] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:48,274] [INFO] Selected 11 target genomes.
[2023-06-08 11:16:48,275] [INFO] Target genome list was writen to GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:16:48,278] [INFO] Task started: fastANI
[2023-06-08 11:16:48,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c54113-0350-4b62-aaab-5231287de5ad/GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:16:54,513] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:54,524] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:16:54,524] [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_003447295.1	s__Acetatifactor sp003447295	95.4788	368	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.04	96.84	0.74	0.71	4	conclusive
GCF_009695995.1	s__Acetatifactor intestinalis	93.5138	489	529	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	89.3295	430	529	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_003584705.1	s__Acetatifactor sp900066565	88.5573	476	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	-
GCA_900772845.1	s__Acetatifactor sp900772845	88.0729	432	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_900771995.1	s__Acetatifactor sp900771995	86.6047	431	529	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_900766575.1	s__Acetatifactor sp900766575	85.3984	282	529	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_900554205.1	s__Acetatifactor sp900554205	78.0564	93	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.93	99.93	0.88	0.88	2	-
GCA_015056975.1	s__Acetatifactor sp015056975	77.928	80	529	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_017465845.1	s__Acetatifactor sp017465845	77.3953	110	529	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_002432425.1	s__CAG-510 sp002432425	77.376	96	529	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	97.90	96.14	0.90	0.83	7	-
--------------------------------------------------------------------------------
[2023-06-08 11:16:54,526] [INFO] GTDB search result was written to GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:16:54,526] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:16:54,530] [INFO] DFAST_QC result json was written to GCA_945999845.1_ERR2020014_bin.7_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:16:54,530] [INFO] DFAST_QC completed!
[2023-06-08 11:16:54,530] [INFO] Total running time: 0h0m55s