[2023-03-19 03:50:09,678] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:09,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:09,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference
[2023-03-19 03:50:10,776] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:10,777] [INFO] Task started: Prodigal
[2023-03-19 03:50:10,777] [INFO] Running command: cat /var/lib/cwl/stgcfdd9c6f-b6ea-42b2-8efb-edab4132b2da/OceanDNA-b6711.fa | prodigal -d OceanDNA-b6711/cds.fna -a OceanDNA-b6711/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:35,505] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:35,505] [INFO] Task started: HMMsearch
[2023-03-19 03:50:35,505] [INFO] Running command: hmmsearch --tblout OceanDNA-b6711/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference/reference_markers.hmm OceanDNA-b6711/protein.faa > /dev/null
[2023-03-19 03:50:35,763] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:35,764] [INFO] Found 6/6 markers.
[2023-03-19 03:50:35,786] [INFO] Query marker FASTA was written to OceanDNA-b6711/markers.fasta
[2023-03-19 03:50:35,788] [INFO] Task started: Blastn
[2023-03-19 03:50:35,788] [INFO] Running command: blastn -query OceanDNA-b6711/markers.fasta -db /var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference/reference_markers.fasta -out OceanDNA-b6711/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:36,346] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:36,347] [INFO] Selected 33 target genomes.
[2023-03-19 03:50:36,347] [INFO] Target genome list was writen to OceanDNA-b6711/target_genomes.txt
[2023-03-19 03:50:36,365] [INFO] Task started: fastANI
[2023-03-19 03:50:36,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfdd9c6f-b6ea-42b2-8efb-edab4132b2da/OceanDNA-b6711.fa --refList OceanDNA-b6711/target_genomes.txt --output OceanDNA-b6711/fastani_result.tsv --threads 1
[2023-03-19 03:50:56,232] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:56,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:56,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:56,246] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:56,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:50:56,247] [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
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.6391	123	1036	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.4412	137	1036	95	below_threshold
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	76.4298	90	1036	95	below_threshold
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	76.3976	107	1036	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	76.3744	128	1036	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.3583	132	1036	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.2194	103	1036	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.2157	101	1036	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.213	127	1036	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.2121	90	1036	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.1582	99	1036	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	76.1218	93	1036	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.0734	128	1036	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	76.0705	96	1036	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.0323	127	1036	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	76.0206	99	1036	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.0206	99	1036	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	75.9881	97	1036	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	75.9198	98	1036	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	75.8547	104	1036	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	75.8386	122	1036	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	75.8072	106	1036	95	below_threshold
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	75.7154	51	1036	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	75.6806	51	1036	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	75.6454	73	1036	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	75.4063	51	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:56,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6711/tc_result.tsv
[2023-03-19 03:50:56,247] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:56,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:56,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference/checkm_data
[2023-03-19 03:50:56,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:56,253] [INFO] Task started: CheckM
[2023-03-19 03:50:56,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6711/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6711/checkm_input OceanDNA-b6711/checkm_result
[2023-03-19 03:51:57,884] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:57,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:57,887] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:57,887] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:57,887] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6711/markers.fasta)
[2023-03-19 03:51:57,887] [INFO] Task started: Blastn
[2023-03-19 03:51:57,887] [INFO] Running command: blastn -query OceanDNA-b6711/markers.fasta -db /var/lib/cwl/stg7d2725b8-2c1f-4092-b9c5-6749ee7bf08e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6711/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:58,631] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:58,632] [INFO] Selected 36 target genomes.
[2023-03-19 03:51:58,632] [INFO] Target genome list was writen to OceanDNA-b6711/target_genomes_gtdb.txt
[2023-03-19 03:51:58,674] [INFO] Task started: fastANI
[2023-03-19 03:51:58,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfdd9c6f-b6ea-42b2-8efb-edab4132b2da/OceanDNA-b6711.fa --refList OceanDNA-b6711/target_genomes_gtdb.txt --output OceanDNA-b6711/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:52:20,778] [INFO] Task succeeded: fastANI
[2023-03-19 03:52:20,794] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:52:20,794] [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_009797885.1	s__Croceivirga sp009797885	77.5291	322	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.6563	122	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	76.5517	104	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	76.4838	80	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072105.2	s__Croceivirga radicis	76.451	89	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.98	97.98	0.93	0.93	2	-
GCF_900215465.1	s__Muricauda pacifica_A	76.4368	136	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963865.1	s__Muricauda_A lutaonensis	76.4151	106	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	97.74	97.69	0.86	0.85	5	-
GCF_005937185.1	s__Muricauda algicola	76.3889	127	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	76.3371	113	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.3337	125	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_003269425.1	s__Muricauda maritima	76.2358	102	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	76.2324	100	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	76.2262	126	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_017313225.1	s__Muricauda sp017313225	76.1919	137	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.1745	97	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.1582	99	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306415.1	s__Croceitalea dokdonensis	76.0855	127	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	76.0437	126	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	76.0357	98	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011068285.1	s__Muricauda sp011068285	75.9947	95	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745185.1	s__Muricauda sp000745185	75.9678	121	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	75.9491	96	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003581615.1	s__Muricauda lutimaris	75.8386	122	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	75.8239	80	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	75.8193	105	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000224085.1	s__Muricauda ruestringensis	75.7967	97	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855515.1	s__Euzebyella marina	75.7389	50	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_900177645.1	s__Arenibacter troitsensis	75.6454	73	1036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:52:20,794] [INFO] GTDB search result was written to OceanDNA-b6711/result_gtdb.tsv
[2023-03-19 03:52:20,794] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:52:20,797] [INFO] DFAST_QC result json was written to OceanDNA-b6711/dqc_result.json
[2023-03-19 03:52:20,797] [INFO] DFAST_QC completed!
[2023-03-19 03:52:20,797] [INFO] Total running time: 0h2m11s