[2023-06-08 13:52:04,076] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:52:04,079] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:52:04,079] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference
[2023-06-08 13:52:05,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:52:05,309] [INFO] Task started: Prodigal
[2023-06-08 13:52:05,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg89dec8c5-e99f-4be1-97d4-1af7d07eceab/GCA_945903495.1_TrH-25oct19-128_genomic.fna.gz | prodigal -d GCA_945903495.1_TrH-25oct19-128_genomic.fna/cds.fna -a GCA_945903495.1_TrH-25oct19-128_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:52:09,605] [INFO] Task succeeded: Prodigal
[2023-06-08 13:52:09,606] [INFO] Task started: HMMsearch
[2023-06-08 13:52:09,606] [INFO] Running command: hmmsearch --tblout GCA_945903495.1_TrH-25oct19-128_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference/reference_markers.hmm GCA_945903495.1_TrH-25oct19-128_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:52:09,842] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:52:09,843] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89dec8c5-e99f-4be1-97d4-1af7d07eceab/GCA_945903495.1_TrH-25oct19-128_genomic.fna.gz]
[2023-06-08 13:52:09,870] [INFO] Query marker FASTA was written to GCA_945903495.1_TrH-25oct19-128_genomic.fna/markers.fasta
[2023-06-08 13:52:09,871] [INFO] Task started: Blastn
[2023-06-08 13:52:09,871] [INFO] Running command: blastn -query GCA_945903495.1_TrH-25oct19-128_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference/reference_markers.fasta -out GCA_945903495.1_TrH-25oct19-128_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:10,506] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:10,511] [INFO] Selected 38 target genomes.
[2023-06-08 13:52:10,511] [INFO] Target genome list was writen to GCA_945903495.1_TrH-25oct19-128_genomic.fna/target_genomes.txt
[2023-06-08 13:52:10,518] [INFO] Task started: fastANI
[2023-06-08 13:52:10,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg89dec8c5-e99f-4be1-97d4-1af7d07eceab/GCA_945903495.1_TrH-25oct19-128_genomic.fna.gz --refList GCA_945903495.1_TrH-25oct19-128_genomic.fna/target_genomes.txt --output GCA_945903495.1_TrH-25oct19-128_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:52:30,361] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:30,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:52:30,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:52:30,371] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:52:30,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:52:30,371] [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
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	77.2796	88	720	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	76.8452	56	720	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.1454	66	720	95	below_threshold
Methylocucumis oryzae	strain=Sn10-6	GCA_000963695.1	1632867	1632867	type	True	75.5817	61	720	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:52:30,373] [INFO] DFAST Taxonomy check result was written to GCA_945903495.1_TrH-25oct19-128_genomic.fna/tc_result.tsv
[2023-06-08 13:52:30,373] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:52:30,374] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:52:30,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference/checkm_data
[2023-06-08 13:52:30,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:52:30,408] [INFO] Task started: CheckM
[2023-06-08 13:52:30,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945903495.1_TrH-25oct19-128_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945903495.1_TrH-25oct19-128_genomic.fna/checkm_input GCA_945903495.1_TrH-25oct19-128_genomic.fna/checkm_result
[2023-06-08 13:52:50,834] [INFO] Task succeeded: CheckM
[2023-06-08 13:52:50,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 13:52:50,858] [INFO] ===== Completeness check finished =====
[2023-06-08 13:52:50,858] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:52:50,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945903495.1_TrH-25oct19-128_genomic.fna/markers.fasta)
[2023-06-08 13:52:50,859] [INFO] Task started: Blastn
[2023-06-08 13:52:50,859] [INFO] Running command: blastn -query GCA_945903495.1_TrH-25oct19-128_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d846ed7-e726-451d-9876-5f1d63031b5d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945903495.1_TrH-25oct19-128_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:51,878] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:51,882] [INFO] Selected 6 target genomes.
[2023-06-08 13:52:51,883] [INFO] Target genome list was writen to GCA_945903495.1_TrH-25oct19-128_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:52:51,885] [INFO] Task started: fastANI
[2023-06-08 13:52:51,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg89dec8c5-e99f-4be1-97d4-1af7d07eceab/GCA_945903495.1_TrH-25oct19-128_genomic.fna.gz --refList GCA_945903495.1_TrH-25oct19-128_genomic.fna/target_genomes_gtdb.txt --output GCA_945903495.1_TrH-25oct19-128_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:52:56,478] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:56,489] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 13:52:56,489] [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_003584895.1	s__KS41 sp003584895	86.082	448	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.75	98.03	0.85	0.79	12	-
GCA_903910205.1	s__KS41 sp903910205	84.9626	409	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.01	98.01	0.77	0.77	2	-
GCA_903905335.1	s__KS41 sp903905335	84.8846	425	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.98	98.89	0.85	0.85	5	-
GCA_903934035.1	s__KS41 sp903934035	83.1562	443	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	98.98	0.89	0.84	3	-
GCA_003584875.1	s__KS41 sp003584875	83.0267	429	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.94	98.69	0.84	0.76	9	-
GCA_903938485.1	s__KS41 sp903938485	77.3829	107	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.68	99.39	0.94	0.91	15	-
--------------------------------------------------------------------------------
[2023-06-08 13:52:56,491] [INFO] GTDB search result was written to GCA_945903495.1_TrH-25oct19-128_genomic.fna/result_gtdb.tsv
[2023-06-08 13:52:56,492] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:52:56,495] [INFO] DFAST_QC result json was written to GCA_945903495.1_TrH-25oct19-128_genomic.fna/dqc_result.json
[2023-06-08 13:52:56,495] [INFO] DFAST_QC completed!
[2023-06-08 13:52:56,495] [INFO] Total running time: 0h0m52s