[2023-06-28 13:05:35,937] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:05:35,939] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:05:35,939] [INFO] DQC Reference Directory: /var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference
[2023-06-28 13:05:37,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:05:37,222] [INFO] Task started: Prodigal
[2023-06-28 13:05:37,222] [INFO] Running command: gunzip -c /var/lib/cwl/stgb10c09e2-6eea-4021-83ba-bbed7cb7d33a/GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:05:44,339] [INFO] Task succeeded: Prodigal
[2023-06-28 13:05:44,339] [INFO] Task started: HMMsearch
[2023-06-28 13:05:44,339] [INFO] Running command: hmmsearch --tblout GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference/reference_markers.hmm GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:05:44,583] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:05:44,584] [INFO] Found 6/6 markers.
[2023-06-28 13:05:44,608] [INFO] Query marker FASTA was written to GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 13:05:44,608] [INFO] Task started: Blastn
[2023-06-28 13:05:44,608] [INFO] Running command: blastn -query GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference/reference_markers.fasta -out GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:05:45,263] [INFO] Task succeeded: Blastn
[2023-06-28 13:05:45,269] [INFO] Selected 23 target genomes.
[2023-06-28 13:05:45,269] [INFO] Target genome list was writen to GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 13:05:45,276] [INFO] Task started: fastANI
[2023-06-28 13:05:45,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgb10c09e2-6eea-4021-83ba-bbed7cb7d33a/GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:05:58,080] [INFO] Task succeeded: fastANI
[2023-06-28 13:05:58,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:05:58,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:05:58,088] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:05:58,088] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:05:58,089] [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 callidus	strain=ATCC 27760	GCA_000468015.1	40519	40519	type	True	84.0408	542	784	95	below_threshold
Ruminococcus champanellensis	strain=type strain: 18P13	GCA_000210095.1	1161942	1161942	type	True	77.3455	122	784	95	below_threshold
Ruminococcus champanellensis	strain=JCM 17042	GCA_001312825.1	1161942	1161942	type	True	77.2283	121	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:05:58,091] [INFO] DFAST Taxonomy check result was written to GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 13:05:58,091] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:05:58,091] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:05:58,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference/checkm_data
[2023-06-28 13:05:58,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:05:58,124] [INFO] Task started: CheckM
[2023-06-28 13:05:58,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 13:06:25,063] [INFO] Task succeeded: CheckM
[2023-06-28 13:06:25,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 13:06:25,097] [INFO] ===== Completeness check finished =====
[2023-06-28 13:06:25,098] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:06:25,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 13:06:25,099] [INFO] Task started: Blastn
[2023-06-28 13:06:25,099] [INFO] Running command: blastn -query GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf205f5c7-fa50-4e5b-84b2-736e5cf75916/dqc_reference/reference_markers_gtdb.fasta -out GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:06:26,144] [INFO] Task succeeded: Blastn
[2023-06-28 13:06:26,149] [INFO] Selected 15 target genomes.
[2023-06-28 13:06:26,150] [INFO] Target genome list was writen to GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:06:26,161] [INFO] Task started: fastANI
[2023-06-28 13:06:26,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgb10c09e2-6eea-4021-83ba-bbed7cb7d33a/GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:06:33,522] [INFO] Task succeeded: fastANI
[2023-06-28 13:06:33,532] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:06:33,532] [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_000980705.1	s__Ruminococcus_C sp000980705	98.8637	699	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.76	98.57	0.85	0.78	6	conclusive
GCF_000468015.1	s__Ruminococcus_C callidus	84.0568	541	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	97.99	97.28	0.85	0.77	9	-
GCA_000437175.1	s__Ruminococcus_C sp000437175	81.3084	383	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.59	98.57	0.89	0.87	4	-
GCA_900545285.1	s__Ruminococcus_C sp900545285	81.0913	306	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	98.99	98.98	0.87	0.83	3	-
GCA_000437255.1	s__Ruminococcus_C sp000437255	78.5815	141	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	99.16	99.04	0.92	0.92	3	-
GCA_017472145.1	s__Ruminococcus_C sp017472145	77.8141	149	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480865.1	s__Ruminococcus_C sp017480865	77.586	140	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558835.1	s__Ruminococcus_F sp004558835	76.9453	90	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521325.1	s__UBA3855 sp017521325	76.706	90	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA3855	95.0	98.30	97.64	0.90	0.83	3	-
GCA_015066805.1	s__Firm-04 sp015066805	76.1169	60	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:06:33,534] [INFO] GTDB search result was written to GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 13:06:33,535] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:06:33,538] [INFO] DFAST_QC result json was written to GCA_948467045.1_SRR17622766_bin.35_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 13:06:33,538] [INFO] DFAST_QC completed!
[2023-06-28 13:06:33,538] [INFO] Total running time: 0h0m58s