[2023-03-16 18:09:00,175] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:09:00,175] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:09:00,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference
[2023-03-16 18:09:01,248] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:09:01,249] [INFO] Task started: Prodigal
[2023-03-16 18:09:01,249] [INFO] Running command: cat /var/lib/cwl/stgdafe56d9-dda7-4e6b-a9ab-14ac56f6a5d2/OceanDNA-b1831.fa | prodigal -d OceanDNA-b1831/cds.fna -a OceanDNA-b1831/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:09:23,113] [INFO] Task succeeded: Prodigal
[2023-03-16 18:09:23,113] [INFO] Task started: HMMsearch
[2023-03-16 18:09:23,113] [INFO] Running command: hmmsearch --tblout OceanDNA-b1831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference/reference_markers.hmm OceanDNA-b1831/protein.faa > /dev/null
[2023-03-16 18:09:23,303] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:09:23,304] [INFO] Found 6/6 markers.
[2023-03-16 18:09:23,327] [INFO] Query marker FASTA was written to OceanDNA-b1831/markers.fasta
[2023-03-16 18:09:23,327] [INFO] Task started: Blastn
[2023-03-16 18:09:23,327] [INFO] Running command: blastn -query OceanDNA-b1831/markers.fasta -db /var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference/reference_markers.fasta -out OceanDNA-b1831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:24,167] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:24,168] [INFO] Selected 14 target genomes.
[2023-03-16 18:09:24,168] [INFO] Target genome list was writen to OceanDNA-b1831/target_genomes.txt
[2023-03-16 18:09:24,177] [INFO] Task started: fastANI
[2023-03-16 18:09:24,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgdafe56d9-dda7-4e6b-a9ab-14ac56f6a5d2/OceanDNA-b1831.fa --refList OceanDNA-b1831/target_genomes.txt --output OceanDNA-b1831/fastani_result.tsv --threads 1
[2023-03-16 18:09:37,781] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:37,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:09:37,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:09:37,790] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:09:37,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:09:37,790] [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	88.3201	951	1154	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	78.015	365	1154	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.7034	424	1154	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.3609	274	1154	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3144	344	1154	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.2181	168	1154	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.1842	222	1154	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	75.2897	266	1154	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	75.1459	242	1154	95	below_threshold
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	75.1423	239	1154	95	below_threshold
Streptomyces janthinus	strain=JCM 4387	GCA_014649675.1	67308	67308	type	True	75.0944	240	1154	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	75.0835	365	1154	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	75.0552	152	1154	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	74.7094	50	1154	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:09:37,791] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1831/tc_result.tsv
[2023-03-16 18:09:37,791] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:09:37,791] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:09:37,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference/checkm_data
[2023-03-16 18:09:37,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:09:37,797] [INFO] Task started: CheckM
[2023-03-16 18:09:37,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1831/checkm_input OceanDNA-b1831/checkm_result
[2023-03-16 18:11:18,923] [INFO] Task succeeded: CheckM
[2023-03-16 18:11:18,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:11:18,925] [INFO] ===== Completeness check finished =====
[2023-03-16 18:11:18,926] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:11:18,926] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1831/markers.fasta)
[2023-03-16 18:11:18,927] [INFO] Task started: Blastn
[2023-03-16 18:11:18,927] [INFO] Running command: blastn -query OceanDNA-b1831/markers.fasta -db /var/lib/cwl/stg17228063-87ae-445d-85fd-915dc754a4c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:11:20,317] [INFO] Task succeeded: Blastn
[2023-03-16 18:11:20,318] [INFO] Selected 16 target genomes.
[2023-03-16 18:11:20,318] [INFO] Target genome list was writen to OceanDNA-b1831/target_genomes_gtdb.txt
[2023-03-16 18:11:20,494] [INFO] Task started: fastANI
[2023-03-16 18:11:20,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgdafe56d9-dda7-4e6b-a9ab-14ac56f6a5d2/OceanDNA-b1831.fa --refList OceanDNA-b1831/target_genomes_gtdb.txt --output OceanDNA-b1831/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:11:30,284] [INFO] Task succeeded: fastANI
[2023-03-16 18:11:30,294] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:11:30,294] [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_018969405.1	s__F1-20-MAGs160 sp018969405	79.504	392	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882825.1	s__F1-20-MAGs160 sp018882825	78.5063	284	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	77.8671	499	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	77.8612	285	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403895.1	s__UBA4742 sp002403895	77.8271	285	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__UBA4742	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.7051	424	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705225.1	s__F1-20-MAGs160 sp009705225	77.6777	207	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.41	99.41	0.86	0.86	2	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.6236	419	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703925.1	s__F1-20-MAGs160 sp009703925	77.6198	223	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.5514	511	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185305.1	s__JACPNV01 sp016185305	77.2621	222	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__JACPNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	77.1976	339	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	77.027	319	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	76.762	268	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009785715.1	s__WQVT01 sp009785715	75.8044	108	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__WQVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971185.1	s__RAAP-2 sp018971185	75.7496	102	1154	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:11:30,295] [INFO] GTDB search result was written to OceanDNA-b1831/result_gtdb.tsv
[2023-03-16 18:11:30,295] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:11:30,296] [INFO] DFAST_QC result json was written to OceanDNA-b1831/dqc_result.json
[2023-03-16 18:11:30,296] [INFO] DFAST_QC completed!
[2023-03-16 18:11:30,297] [INFO] Total running time: 0h2m30s