[2023-03-19 00:15:41,730] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference
[2023-03-19 00:15:43,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,449] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,449] [INFO] Running command: cat /var/lib/cwl/stg3e7d93a6-1495-4e9f-80a4-22eca15beb44/OceanDNA-b1232.fa | prodigal -d OceanDNA-b1232/cds.fna -a OceanDNA-b1232/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:15:56,062] [INFO] Task succeeded: Prodigal
[2023-03-19 00:15:56,063] [INFO] Task started: HMMsearch
[2023-03-19 00:15:56,063] [INFO] Running command: hmmsearch --tblout OceanDNA-b1232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference/reference_markers.hmm OceanDNA-b1232/protein.faa > /dev/null
[2023-03-19 00:15:56,266] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:15:56,267] [INFO] Found 6/6 markers.
[2023-03-19 00:15:56,282] [INFO] Query marker FASTA was written to OceanDNA-b1232/markers.fasta
[2023-03-19 00:15:56,284] [INFO] Task started: Blastn
[2023-03-19 00:15:56,284] [INFO] Running command: blastn -query OceanDNA-b1232/markers.fasta -db /var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference/reference_markers.fasta -out OceanDNA-b1232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:15:57,036] [INFO] Task succeeded: Blastn
[2023-03-19 00:15:57,037] [INFO] Selected 34 target genomes.
[2023-03-19 00:15:57,037] [INFO] Target genome list was writen to OceanDNA-b1232/target_genomes.txt
[2023-03-19 00:15:57,064] [INFO] Task started: fastANI
[2023-03-19 00:15:57,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e7d93a6-1495-4e9f-80a4-22eca15beb44/OceanDNA-b1232.fa --refList OceanDNA-b1232/target_genomes.txt --output OceanDNA-b1232/fastani_result.tsv --threads 1
[2023-03-19 00:16:26,954] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:26,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:26,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:26,961] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:26,961] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:26,962] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.0032	103	600	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.5944	85	600	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	75.4278	50	600	95	below_threshold
Actinomadura pelletieri	strain=DSM 43383	GCA_003634705.1	111805	111805	type	True	75.2844	50	600	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	75.2809	56	600	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	75.2063	56	600	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	75.174	51	600	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	75.1558	55	600	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:26,962] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1232/tc_result.tsv
[2023-03-19 00:16:26,962] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:26,962] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:26,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference/checkm_data
[2023-03-19 00:16:26,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:26,966] [INFO] Task started: CheckM
[2023-03-19 00:16:26,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1232/checkm_input OceanDNA-b1232/checkm_result
[2023-03-19 00:16:59,829] [INFO] Task succeeded: CheckM
[2023-03-19 00:16:59,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:16:59,832] [INFO] ===== Completeness check finished =====
[2023-03-19 00:16:59,832] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:16:59,832] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1232/markers.fasta)
[2023-03-19 00:16:59,833] [INFO] Task started: Blastn
[2023-03-19 00:16:59,833] [INFO] Running command: blastn -query OceanDNA-b1232/markers.fasta -db /var/lib/cwl/stg117739fb-a582-48b7-8042-204c8f6a6d73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:01,103] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:01,104] [INFO] Selected 17 target genomes.
[2023-03-19 00:17:01,104] [INFO] Target genome list was writen to OceanDNA-b1232/target_genomes_gtdb.txt
[2023-03-19 00:17:01,116] [INFO] Task started: fastANI
[2023-03-19 00:17:01,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e7d93a6-1495-4e9f-80a4-22eca15beb44/OceanDNA-b1232.fa --refList OceanDNA-b1232/target_genomes_gtdb.txt --output OceanDNA-b1232/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:09,005] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:09,012] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:09,012] [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_014240365.1	s__UBA9410 sp014240365	98.1389	506	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	conclusive
GCA_012961035.1	s__UBA9410 sp012961035	88.5059	507	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_016845305.1	s__UBA9410 sp016845305	80.1372	380	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	79.9152	357	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	79.3216	268	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	79.3179	339	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_002346745.1	s__S20-B6 sp002346745	78.8183	269	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_002717365.1	s__UBA9410 sp002717365	78.5514	236	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381945.1	s__S20-B6 sp014381945	78.2567	239	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687745.1	s__UBA3125 sp002687745	77.6798	173	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.98	96.61	0.89	0.87	5	-
GCA_903919455.1	s__UBA668 sp903919455	76.2106	57	600	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.17	98.79	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:09,012] [INFO] GTDB search result was written to OceanDNA-b1232/result_gtdb.tsv
[2023-03-19 00:17:09,013] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:09,014] [INFO] DFAST_QC result json was written to OceanDNA-b1232/dqc_result.json
[2023-03-19 00:17:09,014] [INFO] DFAST_QC completed!
[2023-03-19 00:17:09,014] [INFO] Total running time: 0h1m27s