[2023-06-28 03:24:51,957] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:24:51,974] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:24:51,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference
[2023-06-28 03:24:54,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:24:54,270] [INFO] Task started: Prodigal
[2023-06-28 03:24:54,271] [INFO] Running command: gunzip -c /var/lib/cwl/stge4fb2a3e-c408-41a9-ad41-ef72a61b054c/GCA_944387875.1_BRZ_MH_bin34_genomic.fna.gz | prodigal -d GCA_944387875.1_BRZ_MH_bin34_genomic.fna/cds.fna -a GCA_944387875.1_BRZ_MH_bin34_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:25:00,962] [INFO] Task succeeded: Prodigal
[2023-06-28 03:25:00,963] [INFO] Task started: HMMsearch
[2023-06-28 03:25:00,963] [INFO] Running command: hmmsearch --tblout GCA_944387875.1_BRZ_MH_bin34_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference/reference_markers.hmm GCA_944387875.1_BRZ_MH_bin34_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:25:01,207] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:25:01,208] [INFO] Found 6/6 markers.
[2023-06-28 03:25:01,236] [INFO] Query marker FASTA was written to GCA_944387875.1_BRZ_MH_bin34_genomic.fna/markers.fasta
[2023-06-28 03:25:01,236] [INFO] Task started: Blastn
[2023-06-28 03:25:01,236] [INFO] Running command: blastn -query GCA_944387875.1_BRZ_MH_bin34_genomic.fna/markers.fasta -db /var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference/reference_markers.fasta -out GCA_944387875.1_BRZ_MH_bin34_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:01,838] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:01,843] [INFO] Selected 25 target genomes.
[2023-06-28 03:25:01,844] [INFO] Target genome list was writen to GCA_944387875.1_BRZ_MH_bin34_genomic.fna/target_genomes.txt
[2023-06-28 03:25:01,863] [INFO] Task started: fastANI
[2023-06-28 03:25:01,863] [INFO] Running command: fastANI --query /var/lib/cwl/stge4fb2a3e-c408-41a9-ad41-ef72a61b054c/GCA_944387875.1_BRZ_MH_bin34_genomic.fna.gz --refList GCA_944387875.1_BRZ_MH_bin34_genomic.fna/target_genomes.txt --output GCA_944387875.1_BRZ_MH_bin34_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:25:15,040] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:15,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:25:15,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:25:15,057] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:25:15,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:25:15,057] [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
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	77.5163	55	830	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.5094	55	830	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.5047	55	830	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.586	80	830	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.5589	71	830	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.5069	63	830	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.1664	52	830	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.1401	69	830	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:25:15,059] [INFO] DFAST Taxonomy check result was written to GCA_944387875.1_BRZ_MH_bin34_genomic.fna/tc_result.tsv
[2023-06-28 03:25:15,059] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:25:15,059] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:25:15,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference/checkm_data
[2023-06-28 03:25:15,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:25:15,094] [INFO] Task started: CheckM
[2023-06-28 03:25:15,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944387875.1_BRZ_MH_bin34_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944387875.1_BRZ_MH_bin34_genomic.fna/checkm_input GCA_944387875.1_BRZ_MH_bin34_genomic.fna/checkm_result
[2023-06-28 03:25:40,138] [INFO] Task succeeded: CheckM
[2023-06-28 03:25:40,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:25:40,173] [INFO] ===== Completeness check finished =====
[2023-06-28 03:25:40,173] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:25:40,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944387875.1_BRZ_MH_bin34_genomic.fna/markers.fasta)
[2023-06-28 03:25:40,174] [INFO] Task started: Blastn
[2023-06-28 03:25:40,174] [INFO] Running command: blastn -query GCA_944387875.1_BRZ_MH_bin34_genomic.fna/markers.fasta -db /var/lib/cwl/stg1089f0cc-f368-40e5-9f55-e5744de82bcd/dqc_reference/reference_markers_gtdb.fasta -out GCA_944387875.1_BRZ_MH_bin34_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:25:41,030] [INFO] Task succeeded: Blastn
[2023-06-28 03:25:41,035] [INFO] Selected 6 target genomes.
[2023-06-28 03:25:41,035] [INFO] Target genome list was writen to GCA_944387875.1_BRZ_MH_bin34_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:25:41,039] [INFO] Task started: fastANI
[2023-06-28 03:25:41,039] [INFO] Running command: fastANI --query /var/lib/cwl/stge4fb2a3e-c408-41a9-ad41-ef72a61b054c/GCA_944387875.1_BRZ_MH_bin34_genomic.fna.gz --refList GCA_944387875.1_BRZ_MH_bin34_genomic.fna/target_genomes_gtdb.txt --output GCA_944387875.1_BRZ_MH_bin34_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:25:45,080] [INFO] Task succeeded: fastANI
[2023-06-28 03:25:45,089] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 03:25:45,089] [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_004553625.1	s__Scatomorpha merdavium	98.7092	727	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.73	98.49	0.92	0.90	6	conclusive
GCA_900546615.1	s__Scatomorpha pullistercoris	84.7009	523	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.45	98.95	0.93	0.93	3	-
GCA_900752445.1	s__Scatomorpha sp900752445	84.6161	439	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.73	99.73	0.90	0.90	2	-
GCA_900544295.1	s__Scatomorpha intestinigallinarum	84.4419	499	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	99.03	98.73	0.92	0.89	6	-
GCA_900545405.1	s__Scatomorpha sp900545405	84.1017	504	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	98.32	98.22	0.88	0.84	4	-
GCA_900546485.1	s__Scatomorpha sp900546485	83.3327	482	830	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Scatomorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:25:45,097] [INFO] GTDB search result was written to GCA_944387875.1_BRZ_MH_bin34_genomic.fna/result_gtdb.tsv
[2023-06-28 03:25:45,097] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:25:45,101] [INFO] DFAST_QC result json was written to GCA_944387875.1_BRZ_MH_bin34_genomic.fna/dqc_result.json
[2023-06-28 03:25:45,101] [INFO] DFAST_QC completed!
[2023-06-28 03:25:45,102] [INFO] Total running time: 0h0m53s