[2023-06-08 02:39:48,037] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:39:48,039] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:39:48,039] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference
[2023-06-08 02:39:51,923] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:39:51,925] [INFO] Task started: Prodigal
[2023-06-08 02:39:51,926] [INFO] Running command: gunzip -c /var/lib/cwl/stga81f76d3-d3fe-433f-866a-08edfdc76632/GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:40:11,006] [INFO] Task succeeded: Prodigal
[2023-06-08 02:40:11,006] [INFO] Task started: HMMsearch
[2023-06-08 02:40:11,006] [INFO] Running command: hmmsearch --tblout GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference/reference_markers.hmm GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:40:11,293] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:40:11,294] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga81f76d3-d3fe-433f-866a-08edfdc76632/GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 02:40:11,326] [INFO] Query marker FASTA was written to GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:40:11,327] [INFO] Task started: Blastn
[2023-06-08 02:40:11,327] [INFO] Running command: blastn -query GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference/reference_markers.fasta -out GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:40:11,838] [INFO] Task succeeded: Blastn
[2023-06-08 02:40:11,842] [INFO] Selected 10 target genomes.
[2023-06-08 02:40:11,843] [INFO] Target genome list was writen to GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:40:11,845] [INFO] Task started: fastANI
[2023-06-08 02:40:11,845] [INFO] Running command: fastANI --query /var/lib/cwl/stga81f76d3-d3fe-433f-866a-08edfdc76632/GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:40:18,084] [INFO] Task succeeded: fastANI
[2023-06-08 02:40:18,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:40:18,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:40:18,094] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:40:18,094] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 02:40:18,094] [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
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	81.0564	412	1074	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	79.5878	359	1074	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.1568	184	1074	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.9657	196	1074	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.8606	173	1074	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:40:18,096] [INFO] DFAST Taxonomy check result was written to GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:40:18,096] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:40:18,097] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:40:18,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference/checkm_data
[2023-06-08 02:40:18,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:40:18,145] [INFO] Task started: CheckM
[2023-06-08 02:40:18,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:41:12,550] [INFO] Task succeeded: CheckM
[2023-06-08 02:41:12,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:41:12,568] [INFO] ===== Completeness check finished =====
[2023-06-08 02:41:12,569] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:41:12,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:41:12,569] [INFO] Task started: Blastn
[2023-06-08 02:41:12,570] [INFO] Running command: blastn -query GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd816996-3b84-4858-915e-3fec5ce0b5fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:41:13,014] [INFO] Task succeeded: Blastn
[2023-06-08 02:41:13,017] [INFO] Selected 13 target genomes.
[2023-06-08 02:41:13,017] [INFO] Target genome list was writen to GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:41:13,022] [INFO] Task started: fastANI
[2023-06-08 02:41:13,022] [INFO] Running command: fastANI --query /var/lib/cwl/stga81f76d3-d3fe-433f-866a-08edfdc76632/GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:41:20,854] [INFO] Task succeeded: fastANI
[2023-06-08 02:41:20,863] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:41:20,863] [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
GCF_000195635.1	s__Bacteroides fluxus	99.1305	772	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	conclusive
GCF_000614125.1	s__Bacteroides rodentium	81.1575	445	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	81.0835	415	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_905203765.1	s__Bacteroides sp905203765	79.8903	273	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155815.1	s__Bacteroides eggerthii	79.6036	355	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_900129655.1	s__Bacteroides clarus	79.5657	351	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000374365.1	s__Bacteroides gallinarum	79.5106	348	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_004342845.1	s__Bacteroides heparinolyticus	78.5576	275	1074	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-08 02:41:20,870] [INFO] GTDB search result was written to GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:41:20,871] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:41:20,875] [INFO] DFAST_QC result json was written to GCA_945877195.1_ERR1855542_bin.37_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:41:20,876] [INFO] DFAST_QC completed!
[2023-06-08 02:41:20,876] [INFO] Total running time: 0h1m33s