[2023-06-29 06:34:22,615] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:34:22,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:34:22,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference
[2023-06-29 06:34:24,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:34:24,289] [INFO] Task started: Prodigal
[2023-06-29 06:34:24,290] [INFO] Running command: gunzip -c /var/lib/cwl/stg658bf03e-3def-4c29-bb4e-d06e0f8cb5c3/GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:34:34,505] [INFO] Task succeeded: Prodigal
[2023-06-29 06:34:34,506] [INFO] Task started: HMMsearch
[2023-06-29 06:34:34,506] [INFO] Running command: hmmsearch --tblout GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference/reference_markers.hmm GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:34:34,780] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:34:34,781] [INFO] Found 6/6 markers.
[2023-06-29 06:34:34,813] [INFO] Query marker FASTA was written to GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 06:34:34,813] [INFO] Task started: Blastn
[2023-06-29 06:34:34,813] [INFO] Running command: blastn -query GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference/reference_markers.fasta -out GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:34:35,476] [INFO] Task succeeded: Blastn
[2023-06-29 06:34:35,493] [INFO] Selected 29 target genomes.
[2023-06-29 06:34:35,493] [INFO] Target genome list was writen to GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 06:34:35,496] [INFO] Task started: fastANI
[2023-06-29 06:34:35,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg658bf03e-3def-4c29-bb4e-d06e0f8cb5c3/GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:34:53,880] [INFO] Task succeeded: fastANI
[2023-06-29 06:34:53,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:34:53,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:34:53,890] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:34:53,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:34:53,890] [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
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	75.8572	51	1220	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	75.8334	50	1220	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:34:53,892] [INFO] DFAST Taxonomy check result was written to GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 06:34:53,893] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:34:53,894] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:34:53,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference/checkm_data
[2023-06-29 06:34:53,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:34:53,935] [INFO] Task started: CheckM
[2023-06-29 06:34:53,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 06:35:27,692] [INFO] Task succeeded: CheckM
[2023-06-29 06:35:27,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:35:27,712] [INFO] ===== Completeness check finished =====
[2023-06-29 06:35:27,713] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:35:27,713] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 06:35:27,713] [INFO] Task started: Blastn
[2023-06-29 06:35:27,713] [INFO] Running command: blastn -query GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd6ff871-1359-440e-975a-d7ae524c9437/dqc_reference/reference_markers_gtdb.fasta -out GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:35:28,803] [INFO] Task succeeded: Blastn
[2023-06-29 06:35:28,807] [INFO] Selected 20 target genomes.
[2023-06-29 06:35:28,807] [INFO] Target genome list was writen to GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:35:28,813] [INFO] Task started: fastANI
[2023-06-29 06:35:28,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg658bf03e-3def-4c29-bb4e-d06e0f8cb5c3/GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:35:40,769] [INFO] Task succeeded: fastANI
[2023-06-29 06:35:40,780] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:35:40,780] [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_910577675.1	s__RGIG4057 sp910577675	80.87	575	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579615.1	s__RGIG4057 sp910579615	79.9844	653	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587085.1	s__RGIG4057 sp910587085	79.9218	299	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585065.1	s__RGIG4057 sp910585065	78.3626	374	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577165.1	s__RGIG4057 sp910577165	78.2228	410	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579465.1	s__SIG307 sp910579465	76.8792	67	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462755.1	s__RGIG4057 sp017462755	76.4174	85	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4057	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585455.1	s__Eisenbergiella sp910585455	75.9165	57	1220	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:35:40,782] [INFO] GTDB search result was written to GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 06:35:40,783] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:35:40,785] [INFO] DFAST_QC result json was written to GCA_948468945.1_SRR17684625_bin.33_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 06:35:40,786] [INFO] DFAST_QC completed!
[2023-06-29 06:35:40,786] [INFO] Total running time: 0h1m18s