[2023-03-16 13:57:23,195] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:57:23,196] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:57:23,196] [INFO] DQC Reference Directory: /var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference
[2023-03-16 13:57:25,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:57:25,058] [INFO] Task started: Prodigal
[2023-03-16 13:57:25,059] [INFO] Running command: cat /var/lib/cwl/stg7a9c06a4-07ef-40f0-905f-42d0917dcec0/OceanDNA-b22479.fa | prodigal -d OceanDNA-b22479/cds.fna -a OceanDNA-b22479/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:57:52,901] [INFO] Task succeeded: Prodigal
[2023-03-16 13:57:52,902] [INFO] Task started: HMMsearch
[2023-03-16 13:57:52,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b22479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference/reference_markers.hmm OceanDNA-b22479/protein.faa > /dev/null
[2023-03-16 13:57:53,154] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:57:53,154] [INFO] Found 6/6 markers.
[2023-03-16 13:57:53,184] [INFO] Query marker FASTA was written to OceanDNA-b22479/markers.fasta
[2023-03-16 13:57:53,185] [INFO] Task started: Blastn
[2023-03-16 13:57:53,185] [INFO] Running command: blastn -query OceanDNA-b22479/markers.fasta -db /var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference/reference_markers.fasta -out OceanDNA-b22479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:57:53,710] [INFO] Task succeeded: Blastn
[2023-03-16 13:57:53,710] [INFO] Selected 30 target genomes.
[2023-03-16 13:57:53,711] [INFO] Target genome list was writen to OceanDNA-b22479/target_genomes.txt
[2023-03-16 13:57:53,728] [INFO] Task started: fastANI
[2023-03-16 13:57:53,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a9c06a4-07ef-40f0-905f-42d0917dcec0/OceanDNA-b22479.fa --refList OceanDNA-b22479/target_genomes.txt --output OceanDNA-b22479/fastani_result.tsv --threads 1
[2023-03-16 13:58:30,214] [INFO] Task succeeded: fastANI
[2023-03-16 13:58:30,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:58:30,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:58:30,225] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:58:30,225] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:58:30,225] [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
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	75.9605	74	1369	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.9221	122	1369	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.8492	114	1369	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	75.7823	106	1369	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	75.7172	142	1369	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	75.7126	71	1369	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	75.6711	111	1369	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.6416	129	1369	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	75.6387	78	1369	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	75.6371	84	1369	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	75.6297	93	1369	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	75.6179	94	1369	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	75.6043	83	1369	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	75.4847	66	1369	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.4661	98	1369	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	75.4579	82	1369	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	75.4153	93	1369	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:58:30,225] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22479/tc_result.tsv
[2023-03-16 13:58:30,225] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:58:30,225] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:58:30,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference/checkm_data
[2023-03-16 13:58:30,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:58:30,233] [INFO] Task started: CheckM
[2023-03-16 13:58:30,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22479/checkm_input OceanDNA-b22479/checkm_result
[2023-03-16 13:59:59,802] [INFO] Task succeeded: CheckM
[2023-03-16 13:59:59,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 13:59:59,805] [INFO] ===== Completeness check finished =====
[2023-03-16 13:59:59,805] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:59:59,806] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22479/markers.fasta)
[2023-03-16 13:59:59,807] [INFO] Task started: Blastn
[2023-03-16 13:59:59,807] [INFO] Running command: blastn -query OceanDNA-b22479/markers.fasta -db /var/lib/cwl/stga8efd013-3d33-43f8-b36c-f1312a28e49c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:00:00,531] [INFO] Task succeeded: Blastn
[2023-03-16 14:00:00,532] [INFO] Selected 28 target genomes.
[2023-03-16 14:00:00,532] [INFO] Target genome list was writen to OceanDNA-b22479/target_genomes_gtdb.txt
[2023-03-16 14:00:01,437] [INFO] Task started: fastANI
[2023-03-16 14:00:01,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a9c06a4-07ef-40f0-905f-42d0917dcec0/OceanDNA-b22479.fa --refList OceanDNA-b22479/target_genomes_gtdb.txt --output OceanDNA-b22479/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:00:42,553] [INFO] Task succeeded: fastANI
[2023-03-16 14:00:42,564] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 14:00:42,564] [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_001027925.1	s__Rhodopirellula islandica	76.0429	82	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901265.1	s__Stieleria baltica_A	75.9846	71	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007752935.1	s__Crateriforma conspicua	75.9221	122	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_000338295.1	s__Rhodopirellula europaea	75.892	86	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_012290005.1	s__Crateriforma spongiae	75.8492	114	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCA_007741535.1	s__Rubripirellula sp007741535	75.7823	106	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	75.7297	70	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	75.7266	141	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	75.6762	126	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	75.6711	111	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	75.6416	129	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	75.6387	78	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008065135.1	s__Roseimaritima ulvae	75.6054	95	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002289565.1	s__Stieleria sp002289565	75.552	119	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	75.5128	131	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	75.4759	97	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	75.4579	82	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_007860175.1	s__Rubripirellula reticaptiva	75.4153	93	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127095.1	s__UBA6163 sp007127095	75.2332	51	1369	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	99.08	99.08	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2023-03-16 14:00:42,564] [INFO] GTDB search result was written to OceanDNA-b22479/result_gtdb.tsv
[2023-03-16 14:00:42,564] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:00:42,566] [INFO] DFAST_QC result json was written to OceanDNA-b22479/dqc_result.json
[2023-03-16 14:00:42,566] [INFO] DFAST_QC completed!
[2023-03-16 14:00:42,566] [INFO] Total running time: 0h3m19s