[2023-06-28 01:18:10,759] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:18:10,761] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:18:10,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference
[2023-06-28 01:18:12,092] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:18:12,093] [INFO] Task started: Prodigal
[2023-06-28 01:18:12,094] [INFO] Running command: gunzip -c /var/lib/cwl/stgbad10ada-eaf0-410a-915d-6a87dc25572f/GCA_019310425.1_ASM1931042v1_genomic.fna.gz | prodigal -d GCA_019310425.1_ASM1931042v1_genomic.fna/cds.fna -a GCA_019310425.1_ASM1931042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:18:24,531] [INFO] Task succeeded: Prodigal
[2023-06-28 01:18:24,531] [INFO] Task started: HMMsearch
[2023-06-28 01:18:24,531] [INFO] Running command: hmmsearch --tblout GCA_019310425.1_ASM1931042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference/reference_markers.hmm GCA_019310425.1_ASM1931042v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:18:24,813] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:18:24,815] [INFO] Found 6/6 markers.
[2023-06-28 01:18:24,855] [INFO] Query marker FASTA was written to GCA_019310425.1_ASM1931042v1_genomic.fna/markers.fasta
[2023-06-28 01:18:24,856] [INFO] Task started: Blastn
[2023-06-28 01:18:24,856] [INFO] Running command: blastn -query GCA_019310425.1_ASM1931042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference/reference_markers.fasta -out GCA_019310425.1_ASM1931042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:18:25,620] [INFO] Task succeeded: Blastn
[2023-06-28 01:18:25,625] [INFO] Selected 31 target genomes.
[2023-06-28 01:18:25,625] [INFO] Target genome list was writen to GCA_019310425.1_ASM1931042v1_genomic.fna/target_genomes.txt
[2023-06-28 01:18:25,631] [INFO] Task started: fastANI
[2023-06-28 01:18:25,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad10ada-eaf0-410a-915d-6a87dc25572f/GCA_019310425.1_ASM1931042v1_genomic.fna.gz --refList GCA_019310425.1_ASM1931042v1_genomic.fna/target_genomes.txt --output GCA_019310425.1_ASM1931042v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:18:52,442] [INFO] Task succeeded: fastANI
[2023-06-28 01:18:52,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:18:52,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:18:52,458] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:18:52,458] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:18:52,458] [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
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.0756	70	1454	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.002	61	1454	95	below_threshold
Methylorubrum rhodesianum	strain=DSM 5687	GCA_014199985.1	29427	29427	type	True	74.8593	64	1454	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.7772	167	1454	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.7655	175	1454	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	74.7541	115	1454	95	below_threshold
Burkholderia gladioli	strain=NBRC 13700	GCA_000739755.1	28095	28095	type	True	74.7504	100	1454	95	below_threshold
Burkholderia gladioli	strain=NCTC12378	GCA_900446225.1	28095	28095	type	True	74.7477	100	1454	95	below_threshold
Burkholderia gladioli	strain=ATCC 10248	GCA_000959725.1	28095	28095	type	True	74.7419	104	1454	95	below_threshold
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	74.738	113	1454	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	74.7231	67	1454	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	74.7187	58	1454	95	below_threshold
Rhodococcus rhodnii	strain=ATCC 35071	GCA_008011915.1	38312	38312	type	True	74.691	56	1454	95	below_threshold
Rhodococcus rhodnii	strain=NBRC 100604	GCA_001894925.1	38312	38312	type	True	74.6624	57	1454	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	74.6425	63	1454	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:18:52,461] [INFO] DFAST Taxonomy check result was written to GCA_019310425.1_ASM1931042v1_genomic.fna/tc_result.tsv
[2023-06-28 01:18:52,461] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:18:52,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:18:52,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference/checkm_data
[2023-06-28 01:18:52,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:18:52,513] [INFO] Task started: CheckM
[2023-06-28 01:18:52,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310425.1_ASM1931042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310425.1_ASM1931042v1_genomic.fna/checkm_input GCA_019310425.1_ASM1931042v1_genomic.fna/checkm_result
[2023-06-28 01:19:31,572] [INFO] Task succeeded: CheckM
[2023-06-28 01:19:31,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 01:19:31,598] [INFO] ===== Completeness check finished =====
[2023-06-28 01:19:31,598] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:19:31,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310425.1_ASM1931042v1_genomic.fna/markers.fasta)
[2023-06-28 01:19:31,599] [INFO] Task started: Blastn
[2023-06-28 01:19:31,599] [INFO] Running command: blastn -query GCA_019310425.1_ASM1931042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1586cbd5-755c-49a4-8020-45f19f1c3b28/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310425.1_ASM1931042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:19:32,873] [INFO] Task succeeded: Blastn
[2023-06-28 01:19:32,878] [INFO] Selected 26 target genomes.
[2023-06-28 01:19:32,878] [INFO] Target genome list was writen to GCA_019310425.1_ASM1931042v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:19:32,894] [INFO] Task started: fastANI
[2023-06-28 01:19:32,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad10ada-eaf0-410a-915d-6a87dc25572f/GCA_019310425.1_ASM1931042v1_genomic.fna.gz --refList GCA_019310425.1_ASM1931042v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310425.1_ASM1931042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:19:49,633] [INFO] Task succeeded: fastANI
[2023-06-28 01:19:49,648] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 01:19:49,648] [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	76.776	176	1454	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_013215605.1	s__JABSQW01 sp013215605	76.6284	195	1454	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_004356735.1	s__SMWR01 sp004356735	76.51	128	1454	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_011055735.1	s__DSOP01 sp011055735	76.293	198	1454	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_013215615.1	s__JABSQX01 sp013215615	76.0621	128	1454	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.051	188	1454	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_016875395.1	s__VGRF01 sp016875395	76.0338	191	1454	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_011051925.1	s__UBA4427 sp011051925	75.8961	87	1454	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960035.1	s__DUBZ01 sp012960035	75.764	71	1454	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__DUBZ01	95.0	99.83	99.83	0.93	0.93	2	-
GCA_016700055.1	s__Kalu-18 sp016700055	74.8832	53	1454	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	74.87	76	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCA_016790695.1	s__JAEUOS01 sp016790695	74.8122	73	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861105.1	s__VBCG01 sp016861105	74.7938	69	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873935.1	s__Spirillospora algeriensis	74.6487	112	1454	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001942465.1	s__Spirillospora sp001942465	74.6484	100	1454	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:19:49,650] [INFO] GTDB search result was written to GCA_019310425.1_ASM1931042v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:19:49,651] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:19:49,655] [INFO] DFAST_QC result json was written to GCA_019310425.1_ASM1931042v1_genomic.fna/dqc_result.json
[2023-06-28 01:19:49,655] [INFO] DFAST_QC completed!
[2023-06-28 01:19:49,655] [INFO] Total running time: 0h1m39s