[2023-03-18 08:31:56,341] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,342] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference
[2023-03-18 08:31:57,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,472] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,472] [INFO] Running command: cat /var/lib/cwl/stgd7ec3616-7d61-48e6-a800-c7803a17f7e3/OceanDNA-b41341.fa | prodigal -d OceanDNA-b41341/cds.fna -a OceanDNA-b41341/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:18,917] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:18,917] [INFO] Task started: HMMsearch
[2023-03-18 08:32:18,917] [INFO] Running command: hmmsearch --tblout OceanDNA-b41341/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference/reference_markers.hmm OceanDNA-b41341/protein.faa > /dev/null
[2023-03-18 08:32:19,120] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:19,121] [INFO] Found 6/6 markers.
[2023-03-18 08:32:19,142] [INFO] Query marker FASTA was written to OceanDNA-b41341/markers.fasta
[2023-03-18 08:32:19,142] [INFO] Task started: Blastn
[2023-03-18 08:32:19,142] [INFO] Running command: blastn -query OceanDNA-b41341/markers.fasta -db /var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference/reference_markers.fasta -out OceanDNA-b41341/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:19,869] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:19,870] [INFO] Selected 23 target genomes.
[2023-03-18 08:32:19,870] [INFO] Target genome list was writen to OceanDNA-b41341/target_genomes.txt
[2023-03-18 08:32:19,883] [INFO] Task started: fastANI
[2023-03-18 08:32:19,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ec3616-7d61-48e6-a800-c7803a17f7e3/OceanDNA-b41341.fa --refList OceanDNA-b41341/target_genomes.txt --output OceanDNA-b41341/fastani_result.tsv --threads 1
[2023-03-18 08:32:35,673] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:35,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:35,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:35,685] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:35,685] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:32:35,685] [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
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.7591	230	1193	95	below_threshold
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	78.6522	261	1193	95	below_threshold
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	78.2004	122	1193	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	78.0647	234	1193	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	77.6479	229	1193	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.6238	137	1193	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	76.7537	88	1193	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.7092	68	1193	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.4653	61	1193	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	76.3935	83	1193	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	76.3885	87	1193	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	76.3477	78	1193	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.3095	81	1193	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	76.2775	67	1193	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	76.1839	85	1193	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.1704	91	1193	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	76.0939	78	1193	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.0737	110	1193	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	76.0588	64	1193	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	76.053	78	1193	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.0336	81	1193	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:35,775] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41341/tc_result.tsv
[2023-03-18 08:32:35,775] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:35,775] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:35,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference/checkm_data
[2023-03-18 08:32:35,776] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:35,821] [INFO] Task started: CheckM
[2023-03-18 08:32:35,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41341/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41341/checkm_input OceanDNA-b41341/checkm_result
[2023-03-18 08:33:30,247] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:30,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:30,250] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:30,251] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:30,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41341/markers.fasta)
[2023-03-18 08:33:30,251] [INFO] Task started: Blastn
[2023-03-18 08:33:30,251] [INFO] Running command: blastn -query OceanDNA-b41341/markers.fasta -db /var/lib/cwl/stg4f3e3887-ae93-448e-b302-88eb77143c86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41341/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:31,505] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:31,506] [INFO] Selected 13 target genomes.
[2023-03-18 08:33:31,506] [INFO] Target genome list was writen to OceanDNA-b41341/target_genomes_gtdb.txt
[2023-03-18 08:33:31,550] [INFO] Task started: fastANI
[2023-03-18 08:33:31,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ec3616-7d61-48e6-a800-c7803a17f7e3/OceanDNA-b41341.fa --refList OceanDNA-b41341/target_genomes_gtdb.txt --output OceanDNA-b41341/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:40,728] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:40,736] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:33:40,736] [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_002298335.1	s__Oleibacter sp002298335	99.9674	1099	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	conclusive
GCF_900156675.1	s__Oleibacter marinus	78.7216	232	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002706025.1	s__UBA2009 sp002706025	78.6972	270	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCA_002733205.1	s__UBA2009 sp002733205	78.5438	261	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCF_007785795.1	s__UBA2009 sp002335285	78.5414	298	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_016132445.1	s__UBA2009 sp016132445	78.5027	273	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	-
GCA_002314145.1	s__UBA2009 sp002314145	78.3773	253	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCA_002331105.1	s__Oleibacter sp002331105	78.3607	217	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	97.07	0.90	0.84	7	-
GCF_000355675.1	s__Thalassolituus oleivorans	78.1698	123	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	-
GCF_000422845.1	s__Oceanobacter kriegii	78.0647	234	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.0393	110	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	76.0142	82	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	75.8358	98	1193	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:40,736] [INFO] GTDB search result was written to OceanDNA-b41341/result_gtdb.tsv
[2023-03-18 08:33:40,736] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:40,738] [INFO] DFAST_QC result json was written to OceanDNA-b41341/dqc_result.json
[2023-03-18 08:33:40,738] [INFO] DFAST_QC completed!
[2023-03-18 08:33:40,738] [INFO] Total running time: 0h1m44s