[2023-06-13 08:30:33,134] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:30:33,140] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:30:33,140] [INFO] DQC Reference Directory: /var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference
[2023-06-13 08:30:34,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:30:34,538] [INFO] Task started: Prodigal
[2023-06-13 08:30:34,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg26b00b8c-4302-45d5-9294-14f0fcb09e3e/GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:30:40,552] [INFO] Task succeeded: Prodigal
[2023-06-13 08:30:40,553] [INFO] Task started: HMMsearch
[2023-06-13 08:30:40,553] [INFO] Running command: hmmsearch --tblout GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference/reference_markers.hmm GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:30:40,904] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:30:40,905] [INFO] Found 6/6 markers.
[2023-06-13 08:30:40,947] [INFO] Query marker FASTA was written to GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 08:30:40,948] [INFO] Task started: Blastn
[2023-06-13 08:30:40,948] [INFO] Running command: blastn -query GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference/reference_markers.fasta -out GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:30:41,649] [INFO] Task succeeded: Blastn
[2023-06-13 08:30:41,653] [INFO] Selected 14 target genomes.
[2023-06-13 08:30:41,653] [INFO] Target genome list was writen to GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 08:30:41,675] [INFO] Task started: fastANI
[2023-06-13 08:30:41,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg26b00b8c-4302-45d5-9294-14f0fcb09e3e/GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:30:50,087] [INFO] Task succeeded: fastANI
[2023-06-13 08:30:50,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:30:50,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:30:50,092] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:30:50,093] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:30:50,093] [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 flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	77.9755	148	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:30:50,095] [INFO] DFAST Taxonomy check result was written to GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 08:30:50,096] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:30:50,096] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:30:50,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference/checkm_data
[2023-06-13 08:30:50,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:30:50,147] [INFO] Task started: CheckM
[2023-06-13 08:30:50,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 08:31:17,054] [INFO] Task succeeded: CheckM
[2023-06-13 08:31:17,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:31:17,080] [INFO] ===== Completeness check finished =====
[2023-06-13 08:31:17,081] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:31:17,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 08:31:17,081] [INFO] Task started: Blastn
[2023-06-13 08:31:17,082] [INFO] Running command: blastn -query GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga66f9537-cd16-4d38-9415-3a0a8ed92026/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:31:18,166] [INFO] Task succeeded: Blastn
[2023-06-13 08:31:18,170] [INFO] Selected 12 target genomes.
[2023-06-13 08:31:18,170] [INFO] Target genome list was writen to GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:31:18,178] [INFO] Task started: fastANI
[2023-06-13 08:31:18,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg26b00b8c-4302-45d5-9294-14f0fcb09e3e/GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:31:23,204] [INFO] Task succeeded: fastANI
[2023-06-13 08:31:23,217] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:31:23,217] [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_900545125.1	s__Ruminococcus sp900545125	99.9254	629	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	99.79	99.79	0.77	0.77	2	conclusive
GCA_017461395.1	s__Ruminococcus sp017461395	80.4302	302	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513795.1	s__Ruminococcus sp017513795	80.181	308	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.92	97.92	0.90	0.90	2	-
GCA_910579835.1	s__Ruminococcus sp910579835	80.0357	313	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462565.1	s__Ruminococcus sp017462565	79.5519	270	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516465.1	s__Ruminococcus sp017516465	79.4948	293	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556875.1	s__Ruminococcus flavefaciens_S	79.4507	117	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371825.1	s__Ruminococcus flavefaciens_L	77.5766	154	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.29	98.12	0.89	0.86	3	-
GCA_016303195.1	s__Ruminococcus sp016303195	77.511	101	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577575.1	s__Ruminococcus sp910577575	77.3284	107	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:31:23,219] [INFO] GTDB search result was written to GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 08:31:23,220] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:31:23,223] [INFO] DFAST_QC result json was written to GCA_938014085.1_SRR1761687_bin.32_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 08:31:23,223] [INFO] DFAST_QC completed!
[2023-06-13 08:31:23,223] [INFO] Total running time: 0h0m50s