[2023-06-28 19:48:04,295] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:04,297] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:04,297] [INFO] DQC Reference Directory: /var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference
[2023-06-28 19:48:05,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:05,629] [INFO] Task started: Prodigal
[2023-06-28 19:48:05,629] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf486af6-d0ff-4753-89f2-422178495fe6/GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:34,417] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:34,417] [INFO] Task started: HMMsearch
[2023-06-28 19:48:34,418] [INFO] Running command: hmmsearch --tblout GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference/reference_markers.hmm GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:34,702] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:34,703] [INFO] Found 6/6 markers.
[2023-06-28 19:48:34,744] [INFO] Query marker FASTA was written to GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 19:48:34,744] [INFO] Task started: Blastn
[2023-06-28 19:48:34,744] [INFO] Running command: blastn -query GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference/reference_markers.fasta -out GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:35,355] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:35,360] [INFO] Selected 23 target genomes.
[2023-06-28 19:48:35,361] [INFO] Target genome list was writen to GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 19:48:35,369] [INFO] Task started: fastANI
[2023-06-28 19:48:35,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf486af6-d0ff-4753-89f2-422178495fe6/GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:49,241] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:49,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:49,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:49,251] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:49,251] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:48:49,251] [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
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.11	56	1536	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.0798	56	1536	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.6261	57	1536	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:49,254] [INFO] DFAST Taxonomy check result was written to GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 19:48:49,254] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:49,254] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:49,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference/checkm_data
[2023-06-28 19:48:49,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:49,305] [INFO] Task started: CheckM
[2023-06-28 19:48:49,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 19:50:07,116] [INFO] Task succeeded: CheckM
[2023-06-28 19:50:07,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:50:07,137] [INFO] ===== Completeness check finished =====
[2023-06-28 19:50:07,138] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:50:07,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 19:50:07,138] [INFO] Task started: Blastn
[2023-06-28 19:50:07,138] [INFO] Running command: blastn -query GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95bc5e8-53fd-48d7-9433-4192a0487910/dqc_reference/reference_markers_gtdb.fasta -out GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:50:07,926] [INFO] Task succeeded: Blastn
[2023-06-28 19:50:07,930] [INFO] Selected 10 target genomes.
[2023-06-28 19:50:07,930] [INFO] Target genome list was writen to GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:50:07,941] [INFO] Task started: fastANI
[2023-06-28 19:50:07,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf486af6-d0ff-4753-89f2-422178495fe6/GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:50:17,944] [INFO] Task succeeded: fastANI
[2023-06-28 19:50:17,957] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:50:17,957] [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_002501065.1	s__Roseibacillus_B sp002501065	99.8821	1438	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	conclusive
GCA_003483645.1	s__Roseibacillus_B sp003483645	92.032	635	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	90.8601	747	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709395.1	s__Roseibacillus_B sp002709395	78.4921	511	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.31	97.31	0.76	0.76	2	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	77.8097	443	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.9638	197	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	76.8036	177	1536	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	98.76	0.87	0.85	4	-
--------------------------------------------------------------------------------
[2023-06-28 19:50:17,960] [INFO] GTDB search result was written to GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 19:50:17,961] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:50:17,964] [INFO] DFAST_QC result json was written to GCA_913045385.1_ERR598946_bin.99_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 19:50:17,964] [INFO] DFAST_QC completed!
[2023-06-28 19:50:17,964] [INFO] Total running time: 0h2m14s