[2023-06-08 00:04:41,099] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:04:41,100] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:04:41,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference
[2023-06-08 00:04:43,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:04:43,294] [INFO] Task started: Prodigal
[2023-06-08 00:04:43,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg431c1cd9-7ac6-462a-969d-50c99f19a3fb/GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:04:47,393] [INFO] Task succeeded: Prodigal
[2023-06-08 00:04:47,394] [INFO] Task started: HMMsearch
[2023-06-08 00:04:47,394] [INFO] Running command: hmmsearch --tblout GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference/reference_markers.hmm GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:04:47,632] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:04:47,634] [INFO] Found 6/6 markers.
[2023-06-08 00:04:47,659] [INFO] Query marker FASTA was written to GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:04:47,659] [INFO] Task started: Blastn
[2023-06-08 00:04:47,660] [INFO] Running command: blastn -query GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference/reference_markers.fasta -out GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:04:48,250] [INFO] Task succeeded: Blastn
[2023-06-08 00:04:48,257] [INFO] Selected 25 target genomes.
[2023-06-08 00:04:48,258] [INFO] Target genome list was writen to GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:04:48,263] [INFO] Task started: fastANI
[2023-06-08 00:04:48,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg431c1cd9-7ac6-462a-969d-50c99f19a3fb/GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:04:59,605] [INFO] Task succeeded: fastANI
[2023-06-08 00:04:59,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:04:59,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:04:59,608] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:04:59,608] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:04:59,608] [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
--------------------------------------------------------------------------------
[2023-06-08 00:04:59,610] [INFO] DFAST Taxonomy check result was written to GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:04:59,610] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:04:59,611] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:04:59,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference/checkm_data
[2023-06-08 00:04:59,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:04:59,637] [INFO] Task started: CheckM
[2023-06-08 00:04:59,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:05:18,909] [INFO] Task succeeded: CheckM
[2023-06-08 00:05:18,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:05:18,928] [INFO] ===== Completeness check finished =====
[2023-06-08 00:05:18,928] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:05:18,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:05:18,929] [INFO] Task started: Blastn
[2023-06-08 00:05:18,929] [INFO] Running command: blastn -query GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8df8a92c-233e-4da1-81a0-9c25c604f91c/dqc_reference/reference_markers_gtdb.fasta -out GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:05:19,680] [INFO] Task succeeded: Blastn
[2023-06-08 00:05:19,684] [INFO] Selected 18 target genomes.
[2023-06-08 00:05:19,684] [INFO] Target genome list was writen to GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:05:19,690] [INFO] Task started: fastANI
[2023-06-08 00:05:19,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg431c1cd9-7ac6-462a-969d-50c99f19a3fb/GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:05:26,082] [INFO] Task succeeded: fastANI
[2023-06-08 00:05:26,104] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:05:26,105] [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_910585705.1	s__Coproplasma sp910585705	98.0992	497	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910587005.1	s__Coproplasma sp910587005	80.3751	193	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578765.1	s__Coproplasma sp910578765	80.3518	207	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587825.1	s__Coproplasma sp910587825	79.6872	194	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578565.1	s__Coproplasma sp910578565	78.7941	199	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579705.1	s__Coproplasma sp910579705	78.5571	174	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013316055.1	s__Coproplasma sp013316055	78.3765	116	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	97.79	97.79	0.95	0.95	2	-
GCA_910579585.1	s__Coproplasma sp910579585	78.3735	122	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014805025.1	s__Coproplasma sp014805025	78.278	121	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587365.1	s__Coproplasma sp910587365	78.2777	155	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588685.1	s__Coproplasma sp910588685	78.0126	128	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578655.1	s__Coproplasma sp910578655	78.0076	119	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586345.1	s__Coproplasma sp910586345	77.9883	138	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587015.1	s__Coproplasma sp910587015	77.9277	147	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576655.1	s__Coproplasma sp910576655	77.8996	162	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003503945.1	s__Coproplasma sp003503945	77.8449	118	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577875.1	s__Coproplasma sp910577875	77.4409	140	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804995.1	s__Coproplasma sp014804995	77.4256	96	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:05:26,107] [INFO] GTDB search result was written to GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:05:26,107] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:05:26,110] [INFO] DFAST_QC result json was written to GCA_947361815.1_SRR15194760_bin.33_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:05:26,110] [INFO] DFAST_QC completed!
[2023-06-08 00:05:26,111] [INFO] Total running time: 0h0m45s