[2023-06-07 19:52:06,319] [INFO] DFAST_QC pipeline started.
[2023-06-07 19:52:06,332] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 19:52:06,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference
[2023-06-07 19:52:07,668] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 19:52:07,669] [INFO] Task started: Prodigal
[2023-06-07 19:52:07,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b57c045-1d75-4380-9a7e-afce07582806/GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 19:52:13,234] [INFO] Task succeeded: Prodigal
[2023-06-07 19:52:13,235] [INFO] Task started: HMMsearch
[2023-06-07 19:52:13,235] [INFO] Running command: hmmsearch --tblout GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference/reference_markers.hmm GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 19:52:13,584] [INFO] Task succeeded: HMMsearch
[2023-06-07 19:52:13,585] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2b57c045-1d75-4380-9a7e-afce07582806/GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-07 19:52:13,620] [INFO] Query marker FASTA was written to GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 19:52:13,620] [INFO] Task started: Blastn
[2023-06-07 19:52:13,620] [INFO] Running command: blastn -query GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference/reference_markers.fasta -out GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:52:14,211] [INFO] Task succeeded: Blastn
[2023-06-07 19:52:14,222] [INFO] Selected 24 target genomes.
[2023-06-07 19:52:14,223] [INFO] Target genome list was writen to GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 19:52:14,226] [INFO] Task started: fastANI
[2023-06-07 19:52:14,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b57c045-1d75-4380-9a7e-afce07582806/GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 19:52:26,854] [INFO] Task succeeded: fastANI
[2023-06-07 19:52:26,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 19:52:26,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 19:52:26,861] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 19:52:26,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 19:52:26,861] [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
Lactimicrobium massiliense	strain=Marseille-P4301	GCA_900343155.1	2161814	2161814	type	True	76.622	66	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 19:52:26,864] [INFO] DFAST Taxonomy check result was written to GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 19:52:26,865] [INFO] ===== Taxonomy check completed =====
[2023-06-07 19:52:26,865] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 19:52:26,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference/checkm_data
[2023-06-07 19:52:26,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 19:52:26,897] [INFO] Task started: CheckM
[2023-06-07 19:52:26,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 19:52:51,952] [INFO] Task succeeded: CheckM
[2023-06-07 19:52:51,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 19:52:51,975] [INFO] ===== Completeness check finished =====
[2023-06-07 19:52:51,976] [INFO] ===== Start GTDB Search =====
[2023-06-07 19:52:51,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 19:52:51,976] [INFO] Task started: Blastn
[2023-06-07 19:52:51,977] [INFO] Running command: blastn -query GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b6f94c5-de71-43d7-a490-753cddc49563/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 19:52:52,832] [INFO] Task succeeded: Blastn
[2023-06-07 19:52:52,836] [INFO] Selected 20 target genomes.
[2023-06-07 19:52:52,836] [INFO] Target genome list was writen to GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 19:52:52,842] [INFO] Task started: fastANI
[2023-06-07 19:52:52,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b57c045-1d75-4380-9a7e-afce07582806/GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 19:53:01,031] [INFO] Task succeeded: fastANI
[2023-06-07 19:53:01,047] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 19:53:01,047] [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_016293365.1	s__Bulleidia sp016293365	88.7781	443	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014610835.1	s__Bulleidia sp900539965	77.5939	114	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.38	98.19	0.87	0.84	4	-
GCA_900315065.1	s__Bulleidia sp900315065	77.3875	92	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.99	99.99	0.97	0.97	2	-
GCA_902786245.1	s__Bulleidia sp902786245	77.073	57	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905201565.1	s__Bulleidia sp905201565	77.0663	63	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761625.1	s__Bulleidia sp902761625	77.0042	52	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516665.1	s__Bulleidia sp012516665	76.9712	50	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766005.1	s__Bulleidia sp902766005	76.8425	68	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766435.1	s__Bulleidia sp902766435	76.516	55	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539825.1	s__Bulleidia sp017539825	76.2873	59	667	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 19:53:01,050] [INFO] GTDB search result was written to GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 19:53:01,050] [INFO] ===== GTDB Search completed =====
[2023-06-07 19:53:01,053] [INFO] DFAST_QC result json was written to GCA_945877405.1_SRR17382105_bin.15_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 19:53:01,053] [INFO] DFAST_QC completed!
[2023-06-07 19:53:01,053] [INFO] Total running time: 0h0m55s