[2023-06-13 11:29:49,173] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:29:49,179] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:29:49,180] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference
[2023-06-13 11:29:50,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:29:50,888] [INFO] Task started: Prodigal
[2023-06-13 11:29:50,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg20fc9f5d-0b25-4087-9393-9e4b7106fc47/GCA_022563595.1_ASM2256359v1_genomic.fna.gz | prodigal -d GCA_022563595.1_ASM2256359v1_genomic.fna/cds.fna -a GCA_022563595.1_ASM2256359v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:30:00,173] [INFO] Task succeeded: Prodigal
[2023-06-13 11:30:00,173] [INFO] Task started: HMMsearch
[2023-06-13 11:30:00,173] [INFO] Running command: hmmsearch --tblout GCA_022563595.1_ASM2256359v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference/reference_markers.hmm GCA_022563595.1_ASM2256359v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:30:00,423] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:30:00,424] [INFO] Found 6/6 markers.
[2023-06-13 11:30:00,461] [INFO] Query marker FASTA was written to GCA_022563595.1_ASM2256359v1_genomic.fna/markers.fasta
[2023-06-13 11:30:00,465] [INFO] Task started: Blastn
[2023-06-13 11:30:00,465] [INFO] Running command: blastn -query GCA_022563595.1_ASM2256359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference/reference_markers.fasta -out GCA_022563595.1_ASM2256359v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:01,092] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:01,096] [INFO] Selected 22 target genomes.
[2023-06-13 11:30:01,096] [INFO] Target genome list was writen to GCA_022563595.1_ASM2256359v1_genomic.fna/target_genomes.txt
[2023-06-13 11:30:01,102] [INFO] Task started: fastANI
[2023-06-13 11:30:01,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg20fc9f5d-0b25-4087-9393-9e4b7106fc47/GCA_022563595.1_ASM2256359v1_genomic.fna.gz --refList GCA_022563595.1_ASM2256359v1_genomic.fna/target_genomes.txt --output GCA_022563595.1_ASM2256359v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:18,316] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:18,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:18,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:18,324] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:30:18,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:30:18,324] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.6756	107	1035	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	74.75	50	1035	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.6582	70	1035	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	74.6472	64	1035	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.6231	77	1035	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:30:18,330] [INFO] DFAST Taxonomy check result was written to GCA_022563595.1_ASM2256359v1_genomic.fna/tc_result.tsv
[2023-06-13 11:30:18,331] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:18,331] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:18,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference/checkm_data
[2023-06-13 11:30:18,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:18,376] [INFO] Task started: CheckM
[2023-06-13 11:30:18,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022563595.1_ASM2256359v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022563595.1_ASM2256359v1_genomic.fna/checkm_input GCA_022563595.1_ASM2256359v1_genomic.fna/checkm_result
[2023-06-13 11:30:50,081] [INFO] Task succeeded: CheckM
[2023-06-13 11:30:50,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:30:50,107] [INFO] ===== Completeness check finished =====
[2023-06-13 11:30:50,107] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:30:50,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022563595.1_ASM2256359v1_genomic.fna/markers.fasta)
[2023-06-13 11:30:50,108] [INFO] Task started: Blastn
[2023-06-13 11:30:50,108] [INFO] Running command: blastn -query GCA_022563595.1_ASM2256359v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe0c7c0c-1036-49fe-8de2-86671064bf6b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022563595.1_ASM2256359v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:50,913] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:50,918] [INFO] Selected 26 target genomes.
[2023-06-13 11:30:50,918] [INFO] Target genome list was writen to GCA_022563595.1_ASM2256359v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:30:50,935] [INFO] Task started: fastANI
[2023-06-13 11:30:50,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg20fc9f5d-0b25-4087-9393-9e4b7106fc47/GCA_022563595.1_ASM2256359v1_genomic.fna.gz --refList GCA_022563595.1_ASM2256359v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022563595.1_ASM2256359v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:31:03,545] [INFO] Task succeeded: fastANI
[2023-06-13 11:31:03,565] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 11:31:03,565] [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_009692185.1	s__SHZT01 sp009692185	76.5918	72	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__SHZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016180765.1	s__JACPAP01 sp016180765	76.5645	89	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACPAP01	95.0	98.48	98.31	0.80	0.76	4	-
GCA_002923375.1	s__HRBIN33 sp002923375	76.2724	78	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__HRBIN33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222115.1	s__AG29 sp003222115	76.1394	111	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177465.1	s__JACOVF01 sp016177465	76.1138	85	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACOVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221045.1	s__AG41 sp003221045	76.0392	57	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	98.20	98.20	0.96	0.96	2	-
GCA_003221005.1	s__AG25 sp003221005	76.0392	78	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG25	95.0	99.09	99.09	0.79	0.79	2	-
GCA_003222135.1	s__20CM-4-69-16 sp003222135	76.0179	95	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-4-69-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011362545.1	s__DSTP01 sp011362545	75.9451	99	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__DSTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220935.1	s__20CM-4-69-16 sp003220935	75.8723	99	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-4-69-16	95.0	99.20	99.20	0.88	0.88	2	-
GCA_017881445.1	s__JADGQX01 sp017881445	75.8391	55	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__RSA9;g__JADGQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220795.1	s__20CM-4-69-16 sp003220795	75.8173	99	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-4-69-16	95.0	99.73	99.73	0.91	0.91	2	-
GCA_013361335.1	s__AG11 sp013361335	75.7839	73	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_003221075.1	s__20CM-2-65-7 sp003221075	75.7648	60	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-2-65-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221995.1	s__AG29 sp003221995	75.7511	77	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223395.1	s__20CM-2-65-7 sp003223395	75.7107	80	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-2-65-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222035.1	s__AG41 sp003222035	75.6652	79	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__AG41	95.0	99.30	99.30	0.94	0.94	2	-
GCA_016209985.1	s__SHZT01 sp016209985	75.6369	84	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__SHZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199245.1	s__JACQHC01 sp016199245	75.5975	67	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JACQHC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889745.1	s__JAGGAG01 sp017889745	75.5766	54	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JAGGAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221985.1	s__20CM-2-65-7 sp003221985	75.4166	64	1035	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__20CM-2-65-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:31:03,568] [INFO] GTDB search result was written to GCA_022563595.1_ASM2256359v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:31:03,569] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:31:03,573] [INFO] DFAST_QC result json was written to GCA_022563595.1_ASM2256359v1_genomic.fna/dqc_result.json
[2023-06-13 11:31:03,573] [INFO] DFAST_QC completed!
[2023-06-13 11:31:03,573] [INFO] Total running time: 0h1m14s