[2023-03-19 04:11:06,928] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference
[2023-03-19 04:11:08,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,646] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,646] [INFO] Running command: cat /var/lib/cwl/stg09583752-a092-4b67-8f84-aa9233eadd4d/OceanDNA-b22935.fa | prodigal -d OceanDNA-b22935/cds.fna -a OceanDNA-b22935/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:39,987] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:39,988] [INFO] Task started: HMMsearch
[2023-03-19 04:11:39,988] [INFO] Running command: hmmsearch --tblout OceanDNA-b22935/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference/reference_markers.hmm OceanDNA-b22935/protein.faa > /dev/null
[2023-03-19 04:11:40,267] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:40,268] [INFO] Found 6/6 markers.
[2023-03-19 04:11:40,297] [INFO] Query marker FASTA was written to OceanDNA-b22935/markers.fasta
[2023-03-19 04:11:40,297] [INFO] Task started: Blastn
[2023-03-19 04:11:40,297] [INFO] Running command: blastn -query OceanDNA-b22935/markers.fasta -db /var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference/reference_markers.fasta -out OceanDNA-b22935/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:40,854] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:40,855] [INFO] Selected 29 target genomes.
[2023-03-19 04:11:40,856] [INFO] Target genome list was writen to OceanDNA-b22935/target_genomes.txt
[2023-03-19 04:11:40,874] [INFO] Task started: fastANI
[2023-03-19 04:11:40,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg09583752-a092-4b67-8f84-aa9233eadd4d/OceanDNA-b22935.fa --refList OceanDNA-b22935/target_genomes.txt --output OceanDNA-b22935/fastani_result.tsv --threads 1
[2023-03-19 04:12:06,150] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:06,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:12:06,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:12:06,155] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:12:06,155] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:12:06,155] [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	75.8506	97	1579	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.4029	63	1579	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.074	65	1579	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:12:06,155] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22935/tc_result.tsv
[2023-03-19 04:12:06,155] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:12:06,156] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:12:06,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference/checkm_data
[2023-03-19 04:12:06,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:12:06,162] [INFO] Task started: CheckM
[2023-03-19 04:12:06,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22935/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22935/checkm_input OceanDNA-b22935/checkm_result
[2023-03-19 04:13:30,164] [INFO] Task succeeded: CheckM
[2023-03-19 04:13:30,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:13:30,168] [INFO] ===== Completeness check finished =====
[2023-03-19 04:13:30,169] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:13:30,169] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22935/markers.fasta)
[2023-03-19 04:13:30,170] [INFO] Task started: Blastn
[2023-03-19 04:13:30,170] [INFO] Running command: blastn -query OceanDNA-b22935/markers.fasta -db /var/lib/cwl/stg953abf7d-c25a-4abb-b0a4-b7fd1ad4c031/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22935/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:13:30,901] [INFO] Task succeeded: Blastn
[2023-03-19 04:13:30,902] [INFO] Selected 26 target genomes.
[2023-03-19 04:13:30,902] [INFO] Target genome list was writen to OceanDNA-b22935/target_genomes_gtdb.txt
[2023-03-19 04:13:31,300] [INFO] Task started: fastANI
[2023-03-19 04:13:31,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg09583752-a092-4b67-8f84-aa9233eadd4d/OceanDNA-b22935.fa --refList OceanDNA-b22935/target_genomes_gtdb.txt --output OceanDNA-b22935/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:13:55,188] [INFO] Task succeeded: fastANI
[2023-03-19 04:13:55,195] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:13:55,195] [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_002724415.1	s__UBA8437 sp002724415	78.7004	756	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445035.1	s__UBA8437 sp003445035	78.6773	785	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	78.5922	737	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_002726205.1	s__GCA-2726205 sp002726205	77.4605	461	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.8354	98	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752535.1	s__Tautonia plasticadhaerens	75.4029	63	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691905.1	s__SIAF01 sp009691905	75.2829	60	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	75.2607	52	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	75.074	65	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.0208	55	1579	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:13:55,195] [INFO] GTDB search result was written to OceanDNA-b22935/result_gtdb.tsv
[2023-03-19 04:13:55,195] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:13:55,196] [INFO] DFAST_QC result json was written to OceanDNA-b22935/dqc_result.json
[2023-03-19 04:13:55,196] [INFO] DFAST_QC completed!
[2023-03-19 04:13:55,197] [INFO] Total running time: 0h2m48s