[2023-03-19 02:02:08,856] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:02:08,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:02:08,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference
[2023-03-19 02:02:09,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:02:09,976] [INFO] Task started: Prodigal
[2023-03-19 02:02:09,976] [INFO] Running command: cat /var/lib/cwl/stgde8fc94f-9070-45b4-a3ea-1529813b41e8/OceanDNA-b22852.fa | prodigal -d OceanDNA-b22852/cds.fna -a OceanDNA-b22852/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:02:42,855] [INFO] Task succeeded: Prodigal
[2023-03-19 02:02:42,855] [INFO] Task started: HMMsearch
[2023-03-19 02:02:42,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b22852/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference/reference_markers.hmm OceanDNA-b22852/protein.faa > /dev/null
[2023-03-19 02:02:43,269] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:02:43,269] [INFO] Found 6/6 markers.
[2023-03-19 02:02:43,308] [INFO] Query marker FASTA was written to OceanDNA-b22852/markers.fasta
[2023-03-19 02:02:43,315] [INFO] Task started: Blastn
[2023-03-19 02:02:43,315] [INFO] Running command: blastn -query OceanDNA-b22852/markers.fasta -db /var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference/reference_markers.fasta -out OceanDNA-b22852/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:02:47,239] [INFO] Task succeeded: Blastn
[2023-03-19 02:02:47,241] [INFO] Selected 15 target genomes.
[2023-03-19 02:02:47,241] [INFO] Target genome list was writen to OceanDNA-b22852/target_genomes.txt
[2023-03-19 02:02:47,302] [INFO] Task started: fastANI
[2023-03-19 02:02:47,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgde8fc94f-9070-45b4-a3ea-1529813b41e8/OceanDNA-b22852.fa --refList OceanDNA-b22852/target_genomes.txt --output OceanDNA-b22852/fastani_result.tsv --threads 1
[2023-03-19 02:03:01,297] [INFO] Task succeeded: fastANI
[2023-03-19 02:03:01,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:03:01,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:03:01,302] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:03:01,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:03:01,302] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.6648	100	1730	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.615	56	1730	95	below_threshold
Symmachiella macrocystis	strain=CA54	GCA_007860075.1	2527985	2527985	type	True	75.5813	61	1730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:03:01,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22852/tc_result.tsv
[2023-03-19 02:03:01,304] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:03:01,304] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:03:01,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference/checkm_data
[2023-03-19 02:03:01,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:03:01,313] [INFO] Task started: CheckM
[2023-03-19 02:03:01,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22852/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22852/checkm_input OceanDNA-b22852/checkm_result
[2023-03-19 02:04:22,821] [INFO] Task succeeded: CheckM
[2023-03-19 02:04:22,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 02:04:22,837] [INFO] ===== Completeness check finished =====
[2023-03-19 02:04:22,837] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:04:22,837] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22852/markers.fasta)
[2023-03-19 02:04:22,839] [INFO] Task started: Blastn
[2023-03-19 02:04:22,839] [INFO] Running command: blastn -query OceanDNA-b22852/markers.fasta -db /var/lib/cwl/stgc5f5e5fb-0b64-4d78-8dfb-b48cb7f9b175/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22852/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:04:23,735] [INFO] Task succeeded: Blastn
[2023-03-19 02:04:23,743] [INFO] Selected 28 target genomes.
[2023-03-19 02:04:23,743] [INFO] Target genome list was writen to OceanDNA-b22852/target_genomes_gtdb.txt
[2023-03-19 02:04:23,785] [INFO] Task started: fastANI
[2023-03-19 02:04:23,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgde8fc94f-9070-45b4-a3ea-1529813b41e8/OceanDNA-b22852.fa --refList OceanDNA-b22852/target_genomes_gtdb.txt --output OceanDNA-b22852/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:04:47,634] [INFO] Task succeeded: fastANI
[2023-03-19 02:04:47,642] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:04:47,642] [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
GCF_007747795.1	s__Maioricimonas rarisocia	75.6648	100	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	75.5662	51	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.5648	83	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.5616	67	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860075.1	s__Symmachiella macrocystis	75.5444	57	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Mal52;g__Symmachiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3771	60	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242525.1	s__Schlesneria sp018242525	75.3382	56	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	75.3246	71	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778115.1	s__SXKJ01 sp005778115	75.2668	76	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.84	99.84	0.89	0.89	2	-
GCA_016125225.1	s__DSVQ01 sp016125225	75.1748	58	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__DSVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.1651	79	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.048	51	1730	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:04:47,644] [INFO] GTDB search result was written to OceanDNA-b22852/result_gtdb.tsv
[2023-03-19 02:04:47,646] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:04:47,649] [INFO] DFAST_QC result json was written to OceanDNA-b22852/dqc_result.json
[2023-03-19 02:04:47,649] [INFO] DFAST_QC completed!
[2023-03-19 02:04:47,649] [INFO] Total running time: 0h2m39s