[2023-03-19 05:19:33,829] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,829] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,829] [INFO] DQC Reference Directory: /var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference
[2023-03-19 05:19:35,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,422] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,422] [INFO] Running command: cat /var/lib/cwl/stg60724c1a-dbd0-450c-9a21-242dc166c2ff/OceanDNA-b22632.fa | prodigal -d OceanDNA-b22632/cds.fna -a OceanDNA-b22632/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:55,331] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:55,331] [INFO] Task started: HMMsearch
[2023-03-19 05:19:55,331] [INFO] Running command: hmmsearch --tblout OceanDNA-b22632/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference/reference_markers.hmm OceanDNA-b22632/protein.faa > /dev/null
[2023-03-19 05:19:55,588] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:55,589] [INFO] Found 6/6 markers.
[2023-03-19 05:19:55,613] [INFO] Query marker FASTA was written to OceanDNA-b22632/markers.fasta
[2023-03-19 05:19:55,614] [INFO] Task started: Blastn
[2023-03-19 05:19:55,614] [INFO] Running command: blastn -query OceanDNA-b22632/markers.fasta -db /var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference/reference_markers.fasta -out OceanDNA-b22632/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:56,176] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:56,178] [INFO] Selected 21 target genomes.
[2023-03-19 05:19:56,178] [INFO] Target genome list was writen to OceanDNA-b22632/target_genomes.txt
[2023-03-19 05:19:56,190] [INFO] Task started: fastANI
[2023-03-19 05:19:56,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg60724c1a-dbd0-450c-9a21-242dc166c2ff/OceanDNA-b22632.fa --refList OceanDNA-b22632/target_genomes.txt --output OceanDNA-b22632/fastani_result.tsv --threads 1
[2023-03-19 05:20:15,488] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:15,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:15,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:15,495] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:15,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:20:15,496] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.7914	67	1012	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.7534	50	1012	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.6609	74	1012	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.632	57	1012	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.4243	79	1012	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.4208	55	1012	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.1797	57	1012	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.1575	55	1012	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.0592	87	1012	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	74.943	52	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:20:15,496] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22632/tc_result.tsv
[2023-03-19 05:20:15,496] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:15,496] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:15,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference/checkm_data
[2023-03-19 05:20:15,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:15,632] [INFO] Task started: CheckM
[2023-03-19 05:20:15,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22632/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22632/checkm_input OceanDNA-b22632/checkm_result
[2023-03-19 05:21:06,956] [INFO] Task succeeded: CheckM
[2023-03-19 05:21:06,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 05:21:06,960] [INFO] ===== Completeness check finished =====
[2023-03-19 05:21:06,960] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:21:06,960] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22632/markers.fasta)
[2023-03-19 05:21:06,960] [INFO] Task started: Blastn
[2023-03-19 05:21:06,960] [INFO] Running command: blastn -query OceanDNA-b22632/markers.fasta -db /var/lib/cwl/stga35d949b-e7ea-4367-b61c-58ab4d0b1902/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22632/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:21:07,754] [INFO] Task succeeded: Blastn
[2023-03-19 05:21:07,755] [INFO] Selected 19 target genomes.
[2023-03-19 05:21:07,755] [INFO] Target genome list was writen to OceanDNA-b22632/target_genomes_gtdb.txt
[2023-03-19 05:21:07,807] [INFO] Task started: fastANI
[2023-03-19 05:21:07,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg60724c1a-dbd0-450c-9a21-242dc166c2ff/OceanDNA-b22632.fa --refList OceanDNA-b22632/target_genomes_gtdb.txt --output OceanDNA-b22632/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:18,020] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:18,030] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:21:18,030] [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_018970605.1	s__QWPN01 sp018970605	78.4637	305	1012	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	78.3376	194	1012	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	78.3331	346	1012	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	78.2793	317	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670825.1	s__QWPN01 sp003670825	78.1823	205	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	78.0781	285	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_903831155.1	s__QWPN01 sp903831155	77.9954	350	1012	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	77.9487	287	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	77.9119	241	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	77.871	225	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	77.8571	262	1012	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	77.8399	321	1012	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	77.5688	303	1012	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_009923125.1	s__RGVT01 sp009923125	77.5409	184	1012	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	77.5315	253	1012	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_018970785.1	s__F1-20-MAGs016 sp018970785	77.1306	206	1012	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	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:18,030] [INFO] GTDB search result was written to OceanDNA-b22632/result_gtdb.tsv
[2023-03-19 05:21:18,031] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:18,032] [INFO] DFAST_QC result json was written to OceanDNA-b22632/dqc_result.json
[2023-03-19 05:21:18,032] [INFO] DFAST_QC completed!
[2023-03-19 05:21:18,032] [INFO] Total running time: 0h1m44s