[2023-03-19 03:50:07,836] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,837] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference
[2023-03-19 03:50:09,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,607] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,608] [INFO] Running command: cat /var/lib/cwl/stge4800b51-ddfd-408f-84f1-17dd325732d7/OceanDNA-b22627.fa | prodigal -d OceanDNA-b22627/cds.fna -a OceanDNA-b22627/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:33,146] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:33,146] [INFO] Task started: HMMsearch
[2023-03-19 03:50:33,147] [INFO] Running command: hmmsearch --tblout OceanDNA-b22627/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference/reference_markers.hmm OceanDNA-b22627/protein.faa > /dev/null
[2023-03-19 03:50:33,398] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:33,398] [INFO] Found 6/6 markers.
[2023-03-19 03:50:33,431] [INFO] Query marker FASTA was written to OceanDNA-b22627/markers.fasta
[2023-03-19 03:50:33,432] [INFO] Task started: Blastn
[2023-03-19 03:50:33,432] [INFO] Running command: blastn -query OceanDNA-b22627/markers.fasta -db /var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference/reference_markers.fasta -out OceanDNA-b22627/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:33,975] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:33,980] [INFO] Selected 20 target genomes.
[2023-03-19 03:50:33,980] [INFO] Target genome list was writen to OceanDNA-b22627/target_genomes.txt
[2023-03-19 03:50:33,991] [INFO] Task started: fastANI
[2023-03-19 03:50:33,991] [INFO] Running command: fastANI --query /var/lib/cwl/stge4800b51-ddfd-408f-84f1-17dd325732d7/OceanDNA-b22627.fa --refList OceanDNA-b22627/target_genomes.txt --output OceanDNA-b22627/fastani_result.tsv --threads 1
[2023-03-19 03:50:50,835] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:50,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:50,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:50,842] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:50,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:50:50,842] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.7071	75	1223	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.613	86	1223	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.4966	77	1223	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.4913	51	1223	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.4124	101	1223	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.2774	82	1223	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0861	103	1223	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.081	80	1223	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:50,842] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22627/tc_result.tsv
[2023-03-19 03:50:50,842] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:50,842] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:50,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference/checkm_data
[2023-03-19 03:50:50,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:50,849] [INFO] Task started: CheckM
[2023-03-19 03:50:50,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22627/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22627/checkm_input OceanDNA-b22627/checkm_result
[2023-03-19 03:51:48,096] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:48,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:48,099] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:48,099] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:48,099] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22627/markers.fasta)
[2023-03-19 03:51:48,099] [INFO] Task started: Blastn
[2023-03-19 03:51:48,099] [INFO] Running command: blastn -query OceanDNA-b22627/markers.fasta -db /var/lib/cwl/stg14c6ed7c-1a43-4e26-8ce3-6f611f6adc26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22627/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:48,850] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:48,851] [INFO] Selected 19 target genomes.
[2023-03-19 03:51:48,851] [INFO] Target genome list was writen to OceanDNA-b22627/target_genomes_gtdb.txt
[2023-03-19 03:51:48,889] [INFO] Task started: fastANI
[2023-03-19 03:51:48,890] [INFO] Running command: fastANI --query /var/lib/cwl/stge4800b51-ddfd-408f-84f1-17dd325732d7/OceanDNA-b22627.fa --refList OceanDNA-b22627/target_genomes_gtdb.txt --output OceanDNA-b22627/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:51:59,931] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:59,942] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:51:59,951] [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_903958265.1	s__QWPN01 sp903958265	78.6041	295	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_003670825.1	s__QWPN01 sp003670825	78.205	217	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	78.1929	416	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	78.0302	375	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669255.1	s__QWPN01 sp003669255	78.0157	211	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872955.1	s__QWPN01 sp016872955	77.9697	318	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	77.9471	307	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	77.8111	362	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853835.1	s__QWPN01 sp017853835	77.68	307	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	77.534	327	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_003671185.1	s__QWPN01 sp003671185	77.5022	278	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789975.1	s__QWPN01 sp005789975	77.4492	277	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_010027105.1	s__RGVT01 sp010027105	77.3873	245	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872555.1	s__F1-20-MAGs016 sp016872555	77.1108	282	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	77.0822	209	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970785.1	s__F1-20-MAGs016 sp018970785	76.9719	200	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791575.1	s__F1-20-MAGs016 sp005791575	76.8113	229	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951635.1	s__QWOP01 sp903951635	76.7508	265	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	99.54	99.51	0.90	0.90	3	-
GCA_003669605.1	s__QWOP01 sp003669605	76.5263	152	1223	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:51:59,951] [INFO] GTDB search result was written to OceanDNA-b22627/result_gtdb.tsv
[2023-03-19 03:51:59,951] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:51:59,953] [INFO] DFAST_QC result json was written to OceanDNA-b22627/dqc_result.json
[2023-03-19 03:51:59,953] [INFO] DFAST_QC completed!
[2023-03-19 03:51:59,953] [INFO] Total running time: 0h1m52s