[2023-06-28 16:23:01,682] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:23:01,685] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:23:01,685] [INFO] DQC Reference Directory: /var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference
[2023-06-28 16:23:02,913] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:23:02,914] [INFO] Task started: Prodigal
[2023-06-28 16:23:02,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg89159567-ada5-4336-81ef-10966904e42e/GCA_019310325.1_ASM1931032v1_genomic.fna.gz | prodigal -d GCA_019310325.1_ASM1931032v1_genomic.fna/cds.fna -a GCA_019310325.1_ASM1931032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:23:17,227] [INFO] Task succeeded: Prodigal
[2023-06-28 16:23:17,228] [INFO] Task started: HMMsearch
[2023-06-28 16:23:17,228] [INFO] Running command: hmmsearch --tblout GCA_019310325.1_ASM1931032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference/reference_markers.hmm GCA_019310325.1_ASM1931032v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:23:17,513] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:23:17,515] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89159567-ada5-4336-81ef-10966904e42e/GCA_019310325.1_ASM1931032v1_genomic.fna.gz]
[2023-06-28 16:23:17,563] [INFO] Query marker FASTA was written to GCA_019310325.1_ASM1931032v1_genomic.fna/markers.fasta
[2023-06-28 16:23:17,564] [INFO] Task started: Blastn
[2023-06-28 16:23:17,564] [INFO] Running command: blastn -query GCA_019310325.1_ASM1931032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference/reference_markers.fasta -out GCA_019310325.1_ASM1931032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:23:18,261] [INFO] Task succeeded: Blastn
[2023-06-28 16:23:18,265] [INFO] Selected 21 target genomes.
[2023-06-28 16:23:18,265] [INFO] Target genome list was writen to GCA_019310325.1_ASM1931032v1_genomic.fna/target_genomes.txt
[2023-06-28 16:23:18,270] [INFO] Task started: fastANI
[2023-06-28 16:23:18,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg89159567-ada5-4336-81ef-10966904e42e/GCA_019310325.1_ASM1931032v1_genomic.fna.gz --refList GCA_019310325.1_ASM1931032v1_genomic.fna/target_genomes.txt --output GCA_019310325.1_ASM1931032v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:23:38,494] [INFO] Task succeeded: fastANI
[2023-06-28 16:23:38,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:23:38,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:23:38,516] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:23:38,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:23:38,516] [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
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.261	70	1639	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.2293	97	1639	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.1493	105	1639	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1222	181	1639	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	75.1009	116	1639	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.0756	83	1639	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	75.0496	73	1639	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	75.0358	75	1639	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.0061	117	1639	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.9811	102	1639	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	74.9571	92	1639	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.9246	99	1639	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.8742	96	1639	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	74.7919	128	1639	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	74.7919	128	1639	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.791	99	1639	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7259	171	1639	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:23:38,518] [INFO] DFAST Taxonomy check result was written to GCA_019310325.1_ASM1931032v1_genomic.fna/tc_result.tsv
[2023-06-28 16:23:38,519] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:23:38,519] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:23:38,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference/checkm_data
[2023-06-28 16:23:38,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:23:38,577] [INFO] Task started: CheckM
[2023-06-28 16:23:38,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310325.1_ASM1931032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310325.1_ASM1931032v1_genomic.fna/checkm_input GCA_019310325.1_ASM1931032v1_genomic.fna/checkm_result
[2023-06-28 16:24:24,635] [INFO] Task succeeded: CheckM
[2023-06-28 16:24:24,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:24:24,661] [INFO] ===== Completeness check finished =====
[2023-06-28 16:24:24,661] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:24:24,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310325.1_ASM1931032v1_genomic.fna/markers.fasta)
[2023-06-28 16:24:24,662] [INFO] Task started: Blastn
[2023-06-28 16:24:24,662] [INFO] Running command: blastn -query GCA_019310325.1_ASM1931032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga718ac6c-76ed-4f01-a20b-6d2a8cbd2566/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310325.1_ASM1931032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:24:25,745] [INFO] Task succeeded: Blastn
[2023-06-28 16:24:25,749] [INFO] Selected 13 target genomes.
[2023-06-28 16:24:25,750] [INFO] Target genome list was writen to GCA_019310325.1_ASM1931032v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:24:25,759] [INFO] Task started: fastANI
[2023-06-28 16:24:25,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg89159567-ada5-4336-81ef-10966904e42e/GCA_019310325.1_ASM1931032v1_genomic.fna.gz --refList GCA_019310325.1_ASM1931032v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310325.1_ASM1931032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:24:35,157] [INFO] Task succeeded: fastANI
[2023-06-28 16:24:35,173] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:24:35,173] [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_002729515.1	s__GCA-2729515 sp002729515	77.5417	374	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356735.1	s__SMWR01 sp004356735	77.1796	193	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__SMWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.8299	299	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.6736	300	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.3264	248	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.1567	278	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.0906	283	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	75.6213	190	1639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615815.1	s__Luteimonas sp016615815	75.1658	77	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.14	98.29	0.98	0.95	3	-
GCF_014236855.1	s__Xanthomonas_A sp014236855	75.0153	95	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	95.82	95.01	0.91	0.88	7	-
GCF_014197395.1	s__Xanthomonas_A translucens_B	74.8705	90	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:24:35,175] [INFO] GTDB search result was written to GCA_019310325.1_ASM1931032v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:24:35,176] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:24:35,181] [INFO] DFAST_QC result json was written to GCA_019310325.1_ASM1931032v1_genomic.fna/dqc_result.json
[2023-06-28 16:24:35,181] [INFO] DFAST_QC completed!
[2023-06-28 16:24:35,181] [INFO] Total running time: 0h1m33s