[2024-01-24 13:01:20,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:20,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:20,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference
[2024-01-24 13:01:21,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:21,731] [INFO] Task started: Prodigal
[2024-01-24 13:01:21,731] [INFO] Running command: gunzip -c /var/lib/cwl/stge68824c7-1e7e-42ba-81a7-a347d2cadc9d/GCF_003429285.1_ASM342928v1_genomic.fna.gz | prodigal -d GCF_003429285.1_ASM342928v1_genomic.fna/cds.fna -a GCF_003429285.1_ASM342928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:33,330] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:33,330] [INFO] Task started: HMMsearch
[2024-01-24 13:01:33,330] [INFO] Running command: hmmsearch --tblout GCF_003429285.1_ASM342928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference/reference_markers.hmm GCF_003429285.1_ASM342928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:33,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:33,639] [INFO] Found 6/6 markers.
[2024-01-24 13:01:33,679] [INFO] Query marker FASTA was written to GCF_003429285.1_ASM342928v1_genomic.fna/markers.fasta
[2024-01-24 13:01:33,680] [INFO] Task started: Blastn
[2024-01-24 13:01:33,680] [INFO] Running command: blastn -query GCF_003429285.1_ASM342928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference/reference_markers.fasta -out GCF_003429285.1_ASM342928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,433] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,437] [INFO] Selected 22 target genomes.
[2024-01-24 13:01:34,437] [INFO] Target genome list was writen to GCF_003429285.1_ASM342928v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,446] [INFO] Task started: fastANI
[2024-01-24 13:01:34,446] [INFO] Running command: fastANI --query /var/lib/cwl/stge68824c7-1e7e-42ba-81a7-a347d2cadc9d/GCF_003429285.1_ASM342928v1_genomic.fna.gz --refList GCF_003429285.1_ASM342928v1_genomic.fna/target_genomes.txt --output GCF_003429285.1_ASM342928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:50,074] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:50,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:50,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:50,091] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:50,091] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:50,091] [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
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	80.8709	315	1480	95	below_threshold
Alteromonas profundi	strain=345S023	GCA_010500865.1	2696062	2696062	type	True	80.3755	158	1480	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	80.3141	298	1480	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	80.0497	229	1480	95	below_threshold
Alteromonas oceani	strain=S35	GCA_003731635.1	2071609	2071609	type	True	79.8647	164	1480	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	79.6286	175	1480	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	79.3969	355	1480	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	79.1436	165	1480	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	78.9305	259	1480	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.8493	152	1480	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.458	146	1480	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	78.22	79	1480	95	below_threshold
Alteromonas flava	strain=P0211	GCA_002807685.1	2048003	2048003	type	True	78.1351	76	1480	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.1301	183	1480	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.0462	164	1480	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.0442	135	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:50,093] [INFO] DFAST Taxonomy check result was written to GCF_003429285.1_ASM342928v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:50,093] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:50,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:50,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference/checkm_data
[2024-01-24 13:01:50,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:50,142] [INFO] Task started: CheckM
[2024-01-24 13:01:50,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003429285.1_ASM342928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003429285.1_ASM342928v1_genomic.fna/checkm_input GCF_003429285.1_ASM342928v1_genomic.fna/checkm_result
[2024-01-24 13:02:25,690] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:25,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:25,716] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:25,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:25,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003429285.1_ASM342928v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:25,718] [INFO] Task started: Blastn
[2024-01-24 13:02:25,718] [INFO] Running command: blastn -query GCF_003429285.1_ASM342928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac7227e2-b25e-4fd4-8721-f7bc6804985a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003429285.1_ASM342928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:26,780] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:26,785] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:26,785] [INFO] Target genome list was writen to GCF_003429285.1_ASM342928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:26,817] [INFO] Task started: fastANI
[2024-01-24 13:02:26,817] [INFO] Running command: fastANI --query /var/lib/cwl/stge68824c7-1e7e-42ba-81a7-a347d2cadc9d/GCF_003429285.1_ASM342928v1_genomic.fna.gz --refList GCF_003429285.1_ASM342928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003429285.1_ASM342928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:40,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:40,564] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:40,564] [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_003429285.1	s__Alteromonas sediminis	100.0	1480	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	conclusive
GCF_006228385.1	s__Alteromonas iocasae	80.779	312	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500865.1	s__Alteromonas profundi	80.3978	157	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014750655.1	s__Alteromonas profundi_A	80.3141	298	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249295.1	s__Alteromonas antoniana	80.0862	226	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644725.1	s__Alteromonas sp015644725	79.8696	440	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249245.1	s__Alteromonas lipotrueiana	79.6031	402	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	79.4043	358	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584565.2	s__Alteromonas sp002729795	79.3164	208	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCF_000213655.1	s__Alteromonas naphthalenivorans	79.3002	167	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.31	95.95	0.86	0.84	6	-
GCF_000378185.1	s__Alteromonas chungwhensis	78.9535	258	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001562115.1	s__Alteromonas stellipolaris	78.9122	177	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.45	98.97	0.97	0.94	8	-
GCF_016405965.1	s__Alteromonas sp016405965	78.9081	174	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	78.7796	152	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_003367475.1	s__Alteromonas aestuariivivens	78.458	146	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	78.4016	167	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_012911815.1	s__Alteromonas ponticola	77.9491	131	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373625.1	s__Alteromonas sp013373625	77.8653	127	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494365.1	s__Alteromonas mangrovi	77.6981	149	1480	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,566] [INFO] GTDB search result was written to GCF_003429285.1_ASM342928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:40,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:40,570] [INFO] DFAST_QC result json was written to GCF_003429285.1_ASM342928v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:40,570] [INFO] DFAST_QC completed!
[2024-01-24 13:02:40,570] [INFO] Total running time: 0h1m20s