[2023-06-08 00:34:52,556] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:34:52,558] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:34:52,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference
[2023-06-08 00:34:53,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:34:53,853] [INFO] Task started: Prodigal
[2023-06-08 00:34:53,853] [INFO] Running command: gunzip -c /var/lib/cwl/stg66517599-11a4-49cd-bc37-d2754b6eb5df/GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:34:57,720] [INFO] Task succeeded: Prodigal
[2023-06-08 00:34:57,720] [INFO] Task started: HMMsearch
[2023-06-08 00:34:57,721] [INFO] Running command: hmmsearch --tblout GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference/reference_markers.hmm GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:34:57,897] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:34:57,898] [INFO] Found 6/6 markers.
[2023-06-08 00:34:57,917] [INFO] Query marker FASTA was written to GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:34:57,917] [INFO] Task started: Blastn
[2023-06-08 00:34:57,917] [INFO] Running command: blastn -query GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference/reference_markers.fasta -out GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:34:58,516] [INFO] Task succeeded: Blastn
[2023-06-08 00:34:58,519] [INFO] Selected 18 target genomes.
[2023-06-08 00:34:58,519] [INFO] Target genome list was writen to GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:34:58,523] [INFO] Task started: fastANI
[2023-06-08 00:34:58,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg66517599-11a4-49cd-bc37-d2754b6eb5df/GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:06,578] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:06,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:06,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:06,582] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:06,583] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:35:06,583] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	80.0154	247	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:35:06,585] [INFO] DFAST Taxonomy check result was written to GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:35:06,588] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:06,589] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:06,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference/checkm_data
[2023-06-08 00:35:06,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:06,616] [INFO] Task started: CheckM
[2023-06-08 00:35:06,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:35:25,113] [INFO] Task succeeded: CheckM
[2023-06-08 00:35:25,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 00:35:25,130] [INFO] ===== Completeness check finished =====
[2023-06-08 00:35:25,130] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:35:25,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:35:25,131] [INFO] Task started: Blastn
[2023-06-08 00:35:25,131] [INFO] Running command: blastn -query GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a293bc2-6826-4c1e-bb8d-7a3a0421b2cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:26,120] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:26,124] [INFO] Selected 13 target genomes.
[2023-06-08 00:35:26,124] [INFO] Target genome list was writen to GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:35:26,167] [INFO] Task started: fastANI
[2023-06-08 00:35:26,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg66517599-11a4-49cd-bc37-d2754b6eb5df/GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:35:30,974] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:30,985] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 00:35:30,985] [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_002491825.1	s__Ruminococcus_E sp002491825	94.0106	316	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003521625.1	s__Ruminococcus_E sp003521625	93.7421	420	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766885.1	s__Ruminococcus_E sp902766885	89.3431	414	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834225.1	s__Ruminococcus_E bromii	80.0154	247	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.59	98.08	0.94	0.90	6	-
GCF_002834235.1	s__Ruminococcus_E bromii_B	79.9274	238	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.64	96.93	0.86	0.80	74	-
GCA_004560275.1	s__Ruminococcus_E sp004560275	79.8152	135	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215855.1	s__Ruminococcus_E sp905215855	79.4886	241	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.72	97.72	0.86	0.84	4	-
GCA_904393835.1	s__Ruminococcus_E sp904393835	79.2444	198	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543095.1	s__Ruminococcus_E sp900543095	79.0494	199	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.93	99.93	0.91	0.91	2	-
GCA_902766775.1	s__Ruminococcus_E sp902766775	78.9615	189	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493635.1	s__Ruminococcus_E sp002493635	78.9005	195	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.92	97.46	0.88	0.85	4	-
GCA_900319655.1	s__Ruminococcus_E sp900319655	78.3083	134	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.18	96.05	0.81	0.70	33	-
GCA_900315195.1	s__Ruminococcus_E sp900315195	78.1829	123	580	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.59	99.19	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-08 00:35:30,987] [INFO] GTDB search result was written to GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:35:30,987] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:35:30,990] [INFO] DFAST_QC result json was written to GCA_945913045.1_SRR11489780_bin.11_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:35:30,990] [INFO] DFAST_QC completed!
[2023-06-08 00:35:30,990] [INFO] Total running time: 0h0m38s