[2023-06-08 07:24:04,385] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:24:04,392] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:24:04,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference
[2023-06-08 07:24:06,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:24:06,260] [INFO] Task started: Prodigal
[2023-06-08 07:24:06,260] [INFO] Running command: gunzip -c /var/lib/cwl/stgf34160d7-fdcc-44f9-887b-3db05aa8cfff/GCA_945877105.1_MoH-02may19-76_genomic.fna.gz | prodigal -d GCA_945877105.1_MoH-02may19-76_genomic.fna/cds.fna -a GCA_945877105.1_MoH-02may19-76_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:24:13,445] [INFO] Task succeeded: Prodigal
[2023-06-08 07:24:13,445] [INFO] Task started: HMMsearch
[2023-06-08 07:24:13,445] [INFO] Running command: hmmsearch --tblout GCA_945877105.1_MoH-02may19-76_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference/reference_markers.hmm GCA_945877105.1_MoH-02may19-76_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:24:13,665] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:24:13,666] [INFO] Found 6/6 markers.
[2023-06-08 07:24:13,692] [INFO] Query marker FASTA was written to GCA_945877105.1_MoH-02may19-76_genomic.fna/markers.fasta
[2023-06-08 07:24:13,692] [INFO] Task started: Blastn
[2023-06-08 07:24:13,692] [INFO] Running command: blastn -query GCA_945877105.1_MoH-02may19-76_genomic.fna/markers.fasta -db /var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference/reference_markers.fasta -out GCA_945877105.1_MoH-02may19-76_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:14,348] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:14,352] [INFO] Selected 12 target genomes.
[2023-06-08 07:24:14,352] [INFO] Target genome list was writen to GCA_945877105.1_MoH-02may19-76_genomic.fna/target_genomes.txt
[2023-06-08 07:24:14,353] [INFO] Task started: fastANI
[2023-06-08 07:24:14,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgf34160d7-fdcc-44f9-887b-3db05aa8cfff/GCA_945877105.1_MoH-02may19-76_genomic.fna.gz --refList GCA_945877105.1_MoH-02may19-76_genomic.fna/target_genomes.txt --output GCA_945877105.1_MoH-02may19-76_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:24:23,172] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:23,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:24:23,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:24:23,187] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:24:23,187] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:24:23,187] [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
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	85.1457	626	722	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	78.7306	304	722	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	78.3863	280	722	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.4613	176	722	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.4667	53	722	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.4486	54	722	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:24:23,189] [INFO] DFAST Taxonomy check result was written to GCA_945877105.1_MoH-02may19-76_genomic.fna/tc_result.tsv
[2023-06-08 07:24:23,190] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:24:23,190] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:24:23,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference/checkm_data
[2023-06-08 07:24:23,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:24:23,224] [INFO] Task started: CheckM
[2023-06-08 07:24:23,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877105.1_MoH-02may19-76_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877105.1_MoH-02may19-76_genomic.fna/checkm_input GCA_945877105.1_MoH-02may19-76_genomic.fna/checkm_result
[2023-06-08 07:24:49,135] [INFO] Task succeeded: CheckM
[2023-06-08 07:24:49,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:24:49,158] [INFO] ===== Completeness check finished =====
[2023-06-08 07:24:49,158] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:24:49,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877105.1_MoH-02may19-76_genomic.fna/markers.fasta)
[2023-06-08 07:24:49,159] [INFO] Task started: Blastn
[2023-06-08 07:24:49,159] [INFO] Running command: blastn -query GCA_945877105.1_MoH-02may19-76_genomic.fna/markers.fasta -db /var/lib/cwl/stg223f21b6-92fb-4ccb-84d8-0a3f73862fc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877105.1_MoH-02may19-76_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:24:50,161] [INFO] Task succeeded: Blastn
[2023-06-08 07:24:50,166] [INFO] Selected 10 target genomes.
[2023-06-08 07:24:50,166] [INFO] Target genome list was writen to GCA_945877105.1_MoH-02may19-76_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:24:50,168] [INFO] Task started: fastANI
[2023-06-08 07:24:50,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgf34160d7-fdcc-44f9-887b-3db05aa8cfff/GCA_945877105.1_MoH-02may19-76_genomic.fna.gz --refList GCA_945877105.1_MoH-02may19-76_genomic.fna/target_genomes_gtdb.txt --output GCA_945877105.1_MoH-02may19-76_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:24:57,421] [INFO] Task succeeded: fastANI
[2023-06-08 07:24:57,430] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:24:57,430] [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_002737115.1	s__Gemmatimonas sp002737115	97.6767	424	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.83	97.76	0.72	0.69	3	conclusive
GCA_903894655.1	s__Gemmatimonas sp903894655	87.7196	471	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900795.1	s__Gemmatimonas sp903900795	87.1247	564	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004105.1	s__Gemmatimonas sp013004105	85.1591	625	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695095.2	s__Gemmatimonas phototrophica	78.744	303	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483225.1	s__Gemmatimonas sp002483225	78.5114	306	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.70	97.70	0.96	0.96	2	-
GCA_016741895.1	s__Gemmatimonas sp016741895	78.5107	288	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010305.1	s__Gemmatimonas aurantiaca	78.3775	280	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017991005.1	s__Gemmatimonas sp017991005	78.1759	199	722	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:24:57,432] [INFO] GTDB search result was written to GCA_945877105.1_MoH-02may19-76_genomic.fna/result_gtdb.tsv
[2023-06-08 07:24:57,432] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:24:57,435] [INFO] DFAST_QC result json was written to GCA_945877105.1_MoH-02may19-76_genomic.fna/dqc_result.json
[2023-06-08 07:24:57,436] [INFO] DFAST_QC completed!
[2023-06-08 07:24:57,436] [INFO] Total running time: 0h0m53s